US20110097742A1 - Contrast agents, methods for preparing contrast agents, and methods of imaging - Google Patents

Contrast agents, methods for preparing contrast agents, and methods of imaging Download PDF

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US20110097742A1
US20110097742A1 US12/935,413 US93541309A US2011097742A1 US 20110097742 A1 US20110097742 A1 US 20110097742A1 US 93541309 A US93541309 A US 93541309A US 2011097742 A1 US2011097742 A1 US 2011097742A1
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contrast agent
protein
metal ion
agent
metal
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Jenny Jie Yang
Zhiren Liu
Shunyi Li
Yubin Zhou
Jie Jiang
Shenghui Xue
Jinjuan Qiao
Lixia Wei
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Georgia State University Research Foundation Inc
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Assigned to GEORGIA STATE UNIVERSITY RESEARCH FOUNDATION reassignment GEORGIA STATE UNIVERSITY RESEARCH FOUNDATION ASSIGNMENT OF ASSIGNORS INTEREST (SEE DOCUMENT FOR DETAILS). Assignors: ZHOU, YUBIN, WEI, LIXIA, JIANG, JIE, QIAO, JIN-JUAN, XUE, SHENGHUI, LI, SHUNYI, LIU, ZHIREN, YANG, Jenny Jie
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    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K49/00—Preparations for testing in vivo
    • A61K49/06—Nuclear magnetic resonance [NMR] contrast preparations; Magnetic resonance imaging [MRI] contrast preparations
    • A61K49/08—Nuclear magnetic resonance [NMR] contrast preparations; Magnetic resonance imaging [MRI] contrast preparations characterised by the carrier
    • A61K49/10—Organic compounds
    • A61K49/14—Peptides, e.g. proteins
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K49/00—Preparations for testing in vivo
    • A61K49/06—Nuclear magnetic resonance [NMR] contrast preparations; Magnetic resonance imaging [MRI] contrast preparations
    • A61K49/08—Nuclear magnetic resonance [NMR] contrast preparations; Magnetic resonance imaging [MRI] contrast preparations characterised by the carrier
    • A61K49/10—Organic compounds
    • A61K49/12—Macromolecular compounds
    • A61K49/126—Linear polymers, e.g. dextran, inulin, PEG
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K49/00—Preparations for testing in vivo
    • A61K49/06—Nuclear magnetic resonance [NMR] contrast preparations; Magnetic resonance imaging [MRI] contrast preparations
    • A61K49/08—Nuclear magnetic resonance [NMR] contrast preparations; Magnetic resonance imaging [MRI] contrast preparations characterised by the carrier
    • A61K49/10—Organic compounds
    • A61K49/14—Peptides, e.g. proteins
    • A61K49/143—Peptides, e.g. proteins the protein being an albumin, e.g. HSA, BSA, ovalbumin
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P35/00—Antineoplastic agents

Definitions

  • Magnetic resonance imaging is a non-invasive technique providing high resolution, three-dimensional images of morphological features as well as functional and physiological information about tissues in vivo. It is capable of detecting abnormalities in deep tissues and allows for whole body imaging. It has emerged as a primary diagnostic imaging technique for human diseases.
  • Exogenous MRI contrast agents are often used to enhance the contrast between pathological and normal tissues by altering the longitudinal and transverse (i.e., T 1 and T 2 ) relaxation times of water protons.
  • the relaxivity (unit capability of the agent to change the relaxation time) of a contrast agent is dependent on several factors including the number of water molecules in the coordination shell, the exchange rate of the coordinated water with the bulk water, and the rotational correlation time ⁇ R of the contrast agent.
  • the MRI contrast agent can have: 1) high relaxivity for high contrast-to-noise ratio (CNR) and dose efficiency, 2) thermodynamic stability, especially metal selectivity for the target ions over excess physiological metal ions, to minimize the release of toxic paramagnetic metal ions, 3) adequate vascular, tissue retention time to allow imaging, and 4) proper excretion from the body.
  • CNR contrast-to-noise ratio
  • thermodynamic stability especially metal selectivity for the target ions over excess physiological metal ions, to minimize the release of toxic paramagnetic metal ions
  • 3) adequate vascular, tissue retention time to allow imaging and 4) proper excretion from the body.
  • One exemplary contrast agent includes: a) a scaffold protein, and b) at least one metal ion chelating site, wherein the scaffold protein includes at least one metal ion chelating site that is already present or is integrated into the scaffold protein, wherein the scaffold protein includes a metal ion bound to a metal ion chelating site, wherein the contrast agent is stable in a physiological environment.
  • One exemplary method of imaging a sample includes: administering at least one of the contrast agent described herein to the sample; introducing the sample to an imaging system; and imaging the sample.
  • One exemplary method for preparing a contrast agent includes: a) selecting a scaffold protein; b) constructing at least one metal ion chelating site; c) operatively embedding the metal ion binding site into the protein, wherein the metal ion has contrast agent properties, and d) attaching at least one polyethylene glycol (PEG) to the scaffold protein.
  • PEG polyethylene glycol
  • FIG. 1.1 Schematic descriptions of different classes of MRI contrast agents and simulation of T 1 relaxivity.
  • FIG. 1.1( a ) Different constructs of MRI contrast agents.
  • ⁇ Rs slow ⁇ R due to its internal mobility;
  • Schematic description of the design of reported MRI contrast agents by directly coordinating Gd 3+ ions to ligand residues on a rigid protein frame to eliminate the high internal mobility.
  • FIG. 1.1( b ) Simulated T 1 relaxivity at the given rotational correlation time ⁇ R (100 ps, below, or 10 ns, above), water dwelling time ⁇ m , correlation time of splitting ⁇ v (1 and 10 ps, solid and dashed lines, respectively), and mean square zero field splitting energy ⁇ 2 (10 18 s ⁇ 2 ).
  • the ⁇ m valves are 10 ⁇ 10 ( ⁇ ), 10 ⁇ 9 ( ⁇ ), and 10 ⁇ 8 s ( ⁇ ) for 100 ps ⁇ R and 10 ⁇ 9 ( ⁇ ), 10 ⁇ 8 ( ⁇ ), and 10 ⁇ 7 s ( ⁇ ) for 10 ns ⁇ R according to the theory developed by Blombergen, Solomon (refs 6 and 7 in Example 1).
  • the water coordination number, q is assumed to be 1 and the agent concentration is 0.001 M. See on-line supporting materials for r1 and r2 simulations.
  • FIG. 1.1( c ) Modeled structure of designed Gd 3+ -CA1.CD2 based on the designed NMR structure 1T6W (ref 31 in Example 1). Ligand residues E15, E56, D58, D62 and D64 at the B, E, and D ⁇ -strands of the host protein CD2 are shown in red.
  • FIG. 1.2 Comparison of in vitro relaxivity between DTPA and designed contrast agents.
  • FIG. 1.2( a ) MR images produced using Spin-echo sequence, TR 6000 ms, TI 960 ms, TE 7.6 ms at 3T.
  • Samples are 1) dH 2 O, 2) 10 mM Tris-HCl pH 7.4, 3) 0.10 mM Gd-DTPA in H 2 O, 4) 0.10 mM Gd-DTPA in 10 mM Tris-HCl pH 7.4, 5) 0.10 mM Gd 3+ and CD2, 6) 0.077 mM Gd-CA4.CD2, 7) 0.050 mM Gd-CA2.CD2, 8) 0.10 mM Gd-CA9.CD2, 9) 0.020 mM Gd-CA1.CD2, and 10) 0.050 mM Gd-CA1.CD2.
  • FIG. 1.2( b ) Proton relaxivity values of Gd-CA1.CD2 (r 1 , solid black; r 2 , cross) and Gd-DPTA (r 1 , shield; r 2 , open) at indicated field strength were measured.
  • FIG. 1.2( c ) In vitro relaxivity of contrast agents Gd-DPTA (DTPA), Gd-CA1.CD2 (CA1) and Gd-CA2.CD2 (CA2) in the absence of Ca 2+ (black and grey), presence of 1 mM Ca 2+ (left strip and open) and 10 mM Ca 2+ (right strip and cross) at 3T.
  • T 1 (black, left & right strips) and T 2 (grey, open and cross) were determined using a Siemens whole-body MR system.
  • FIG. 1.3 Dynamic properties and hydration water number of designed contrast agents.
  • FIG. 1.3( a ) S 2 order values of the engineered metal binding protein. The positions of ligand residues are shown in vertical bars. Order factors of CA2-CD2 with discontinuous ligand residues have the same dynamic properties as the scaffold protein. Arrows indicate the position of ligand residues.
  • FIG. 1.3( b ) Measurement of coordination water number by monitoring Tb 3+ life time. Luminescence decay lifetime was obtained by fitting the acquired data in both H 2 O and D 2 O with a mono-exponential decay function.
  • FIG. 1.4 In vivo MR images and biodistribution of designed contrast agents.
  • FIG. 1.4( b ) The MRI signal intensity changes at kidney ( ⁇ ), liver ( ⁇ ), and muscle ( ⁇ ) as a function of time. The 0 refers to the pre-injection.
  • FIG. 1.4( a ) MR images of mouse (26 g) pre (left) and 40 minutes post (right) the injection of 50 ⁇ L, of 1.2 mM Gd-CA1.CD2 through the tail vein. The MRI was performed using a spin echo sequence with
  • FIG. 1.5 The ESI-TOF MS spectrum of Gd-CA1.CD2.
  • the ESI-TOF MS spectra of the complex were recorded by Q-TOF Micro Mass Spectrometer (Micromass).
  • FIG. 1.6 Measurement of metal binding constants. Gd 3+ binding affinity ( FIG. 1.6 a ) and Zn 2+ binding affinity ( FIG. 1.6 b ) of CA1.CD2 measured by dye competition assays. CA1.CD2 stock solution was gradually added into the 1:1 dye-metal complex to compete for the dye-bound metal ions. The insets show the titration curve for the dye indicators fluo 5N ( FIG. 1.6 a ) and FluoZin ( FIG. 1.6 b ), respectively.
  • FIG. 1.6 c La 3+ binding affinity obtained by Aromatic residue sensitized Tb 3+ luminescence energy transfer. The Tb 3+ fluorescence of a protein-Tb 3+ mixture decreases with the addition of La 3+ .
  • the La 3+ concentrations are 0, 0.30, 0.76, 5.95, 11.03, and 28.95 ⁇ M from top to bottom.
  • the Tb 3+ fluorescence decrease competition was fitted (line) by a normal competition plus a nonspecific quenching effect (inset).
  • FIG. 1.7 MRI imaging of CA1.CD2 at 9.4 T.
  • FIG. 1.7( a ) MR images of CD-1 mouse (26 g) (four mice were imaged) at 9.4T field using Gd-CA1.CD2 as a T 2 -weighted contrast agent. The images were recorded pre-(i) and 2 hours post-(ii & iii) injection of 50 ⁇ l of 1.2 mM Gd-CA1.CD2 agent through the tail vein. MR images were recorded using a multi-echo Carr-Purcell-Meiboom-Gill (CPMG) sequence. The in-plane resolution is 0.2 ⁇ 0.3 ⁇ 1.0 mm.
  • CPMG Carr-Purcell-Meiboom-Gill
  • the MRI intensity in muscle at 10 minutes post contrast administration was defined as 1.
  • MRI intensities at other tissue sites were normalized to the muscle intensity.
  • FIG. 1.8 Detection of CA1.CD2 in serum and cytotoxicity of CA1.CD2.
  • FIG. 1.8( a ) Sandwich ELISA detection of CA1.CD2 in mouse blood using OX45 and PabCD2. PabCD2 was used as the capture antibody and OX45 was used as the detection antibody in the sandwich-ELISA experiments. Serum samples were obtained from test mice at 0, 0.5, 1.0, 2, and 3 hours post injection (tail vein) of Gd-CA1.CD2 ( ⁇ 1.0 ⁇ mole/kg). The amounts of CA1.CD2 are expressed as percentages of the injected dose. Calculations are based on the assumption that the total blood volume is 8% of each individual mouse body weight. FIG.
  • 1.8( b ) The cytotoxicity of designed protein Gd-CA1.CD2.
  • the SW480 cells were grown under standard conditions (1 ⁇ 10 4 cells in 100 ⁇ l medium). The cells were treated by addition of wild type CD2 (stripe bars), CA1.CD2 (grey bars), Gd-CA1.CD2 (black bars), and Gd-DTPA (cross bars) with concentrations of 30 ⁇ M (left panel) or 50 ⁇ M (right panel).
  • the open bars are controls where cells were treated with PBS buffer. The cells were incubated with the treatments for 48 hours. The cells were then subjected for MTT assay. The results were presented as percentages of viable cells using the cells that were treated with buffer alone (filled bars) as a reference (100%).
  • the cell lines SW620 and HEK293 were similarly examined.
  • FIG. 2.1( a ) Illustrates the model structure of the designed contrast agent CA1.CD2 with eight Lys residues highlighted. The solvent accessibility calculated by Getarea is also listed.
  • FIG. 2.1 ( b ) Examples of PEGylation reagents used with different chain lengths and molecular weights and related chemical reactions.
  • FIG. 2.2 (top) illustrates a FPLC profile for the separation of pegylated protein CA1.CD2 with P12K and reaction mixture by gel filtration column. (bottom) The SDS gel of FPLC fractions (peaks 123) of CA1.CD2 pegylated with P40 stained by idiol (left) and commassie blue (right).
  • FIG. 2.3 The SDS gel stained by commassie blue (middle) for protein and iodine (top) for PEG moiety with 5:1 PEG:protein using the preactivated PEG reagents.
  • CA1.CD2 was Pegylated mainly with 3, 4, 5 PEG. (bottom) MALD-Mass analyses of mixture after PEGylation with PEG40.
  • FIG. 2.4 Illustrates the conformational analysis of PEGylaed CA1.CD2.
  • Trp emission fluorescence spectrum of CA1.CD2 is similar to that PEGylated CA1.CD2-PEG12 and CA1.CD2-PEG40 excited at 280 nm.
  • the Terbium-sensitized energy transfer was used to monitor the binding of metal ions in the designed binding pocket. The Tb3+ emission is gradually increased upon addition of terbium excited at 280 nm.
  • FIG. 2.5 Pegylated CA1.CD2-P40 remains intact after incubate with human serum for 24 hours at 37° C. monitored by SDS Page.
  • FIG. 2.6 R1 (left) and R2 (right) relaxivity values of CA1.CD2 alone, pegylated with P12, and P40 compared with DTPA at different field strengths (0.47, 3.0, 9.4, and 11.4T).
  • FIG. 2.7 Illustrates ELISA (left) or western blot (right) analyses of antibody produced in rabbit serum after i.p. injection of 3 ng/kg of protein CA1.CD2 or PEGylated CA1.CD2 (PEGCA1.CD2).
  • Pre is the serum from pre-bleeding before antigen injection.
  • CA1.CD2 was mixed with adjuvant (CA1.CD2+Ad) or with buffer saline (CA1.CD2+Sal) before injection.
  • PabCD2 is the anti-serum from rabbits produced by a commercial source use CD2 as antigen.
  • the open bars are the first bleed after first injection.
  • the gray bars are the second bleed after second injection.
  • the rabbit blood was taken 3 weeks after each injection.
  • the error bars are standard deviations of four measurements.
  • Western blots were performed with anti-serum (1st bleed) from rabbits that were injected; CA1.CD2 mixed with buffered saline (left panel, CA1.CD2+Sal), CA1.CD2 mixed with adjuvant (middle panel, CA1.CD2+Ad), and the PEGylated CA1.CD2 (right panel, PEG-CA1.CD2).
  • the Western blots experiments were carried out with 0.5 mg of PEGylated CA1.CD2 (PEG-CA1.CD2) or unmodified CA1.CD2 (CA1.CD2). Arrow indicates the position of the detected protein bands 19 hours post injection.
  • FIG. 2.8 Table 2.1 is a summary of water number in CA1.CD2 and its variants.
  • FIG. 3.1 Illustrates the development of MRI contrast agents by modifying natural calcium binding proteins such as calmodulin with four metal binding sites.
  • FIG. 3.2 Illustrates the determination of Gd 3+ stability constant of CaM variants.
  • CaM titration FIG. 3.2A
  • FIG. 3.2B curve fitting with Fura-2 fluorescence spectra. The measurement was performed at 20 mM Gd 3+ and 20 mM Fura-2 with 10 mM Tris and pH 7.4.
  • FIG. 3.2( c ) The meal selectivity of CBPP (left) and CBPP56 (right).
  • FIG. 3.3 Illustrates the SDS gel of PEGylation of CaM variants with P12 (lanes 1-6), P40 (lanes 7-10), P5K (Lanes 11-14), and P40 (lanes 15-17) at different reaction time with PEG:protein 5:1 ratio stained by Idiol (top A) and commossie blue (bottom B).
  • FIG. 3.4 Illustrates the separation of PEGylation of CaM variants-P12 with mono-Q column (left) and UV absorption spectrum of purified protein (right).
  • FIG. 3.5 Illustrates Tyr emission spectra of CAM variant without and with PEGYlation by P12K excited at 280 nm ( FIG. 3.5A ) Emission spectra of Tb fluorescence of CAM variant ( FIG. 3.5B ) and its PEGylated one in the presence of 0 (bottom), 5 uM (middle), and 20 uM of protein (top) excited at 280 nm ( FIG. 3.5C ).
  • FIG. 3.6 Shows the SDS PAGE results of serum stability for new designed protein based MRI Contrast Agents at different time points incubating with serum at 37° C. ( FIG. 3.6A ). CBP1; (FIG. 3 . 6 B).CBPP.
  • FIG. 3.7 Illustrates MRI images of Mice at 4.7T with tail vein injection of 6 mM CBP1 at 0, 10, and 30 mins post injection (top). Relative MRI intensity at different organs (bottom).
  • FIG. 3.8 Illustrates relaxivity of CBP1 at 0.47 T. Both R1 and R2 values are 5-8 fold higher than DTPA.
  • FIG. 3.9 Illustrates MRI images of Mice at 4.7T with tail vein injection of 6 mM CBP1-P40 at 0, and 13 mins post injection at slice 3 (top) and slice 4 (bottom). (right) These graphs illustrate the relative MRI intensity at different organs.
  • FIG. 3.10 Illustrates Table 3.1, which shows the dissociation constant of C 2+ , Tb 3+ and Gd 3+ to CBPP were measured by Fluorescence spectroscopy.
  • the intrinsic tryptophan fluorescence change were used to monitor the binding process between CBP1/CBPP and metal.
  • the aromatic residue-sensitized Tb 3+ fluorescence at 545 nm were applied to monitor the process of Tb 3+ binding to CBP1/CBPP and the variants.
  • FIG. 4.1 The affibody that can specifically bind to Her2 biomarker on the cancer cells was fused to the C-terminal of the protein contrast agent CA1.CD2 with a designed Gd 3+ binding site (denoted as CA1-Affi). This contrast agent was surface modified with PEG40 to reduce immunogenesity and increase solubility and serum stability (PEG-CA1-Affi). The affibody was further conjugated with near infra-red dye Cy5.5 via a Cys at the C-terminal to generate a dual labeled contrast agent PEG-CA1-Affi-Cy5.5.
  • FIG. 4.2 Contrast agent with PeGylation (PEG-CA1-affi) and without PeGylation (CA1-Aff) is able to bind to the positive cell line AU565 with membrane staining at 4 C (top right) and both membrane and cytosol staining at 37 C (top left). This developed contrast agent does not bind to negative cell line EMT-6 at either 4 or 37 C. (Bottom right) Near IR labeled contrast agent PEG-CA1-affi-Cy5.5 is able to bind to positive cell lines AU565 and AKOV-3 with NIR fluorescence signal. These data suggest that our contrast agent fused with the affibody can target to HER2 positive tumor cell lines specifically. PEGylation does not change the target capability to the cancer cell. At 37° C., the contrast agent is endocytosized.
  • FIG. 4.3 Specific targeting to the positive cancer cell line (AU565) and negative cell line (EMT6) monitored by 153 Gd ( FIG. 4.3A ) and ELISA ( FIG. 4.3B ). Similar radioactivity (CPM) of the contrast agents without PEGylation (CA1-Affi) and with PEGylation (PEG-CA1-Affi) at 75, 150, 375 nM were observed for AU565 cell line. Under identical conditions, negative cell line EMT has a small radioactivity after incubating with 153 Gd labeled contrast agent.
  • CPM radioactivity
  • FIG. 4.4 Breast cancer biomarker HER2 positive tumor and negative tumor were implanted on the left and right back in nude mice.
  • 5 mM contrast agent CA1.Affi-P40 (100 fold lower than clinic used DTPA) was injected via tail vein.
  • MRI images at 4.7 T using fast spin echo were acquired before injection, and at 5 min, 30 min, 3 hr, 24 hr and 52 hr post injection.
  • Positive tumor shows a strong contrast after 30 mins and peaked at 24 hour with about 35% enhancement. Contrast capability was decreased after 52 hours, suggesting that the contrast agent was secreted out of the animal. This mouse was alive and looks normal after 52 hours MRI scanning.
  • FIG. 4.5 Nude mice were inoculated with negative cell line MDA-MB-231 and positive cell line SKOV-3 (top). The cell number for each spot was about 5 ⁇ 10 6 .
  • the specific binding of positive tumor on the right upon injection of the dual labeled contrast PeG-CA1-Affi-Cy5.5 can be visualized using Kodak NIR in vivo FX-pro animal imaging system 21 hours poster injection.
  • (middle) Traverse MR images of tumor mice at 4.7T with fast spin echo obtained at 3 min., 35 min., and 21 hours following administration of the contrast agent.
  • Bottom right The intensity enhancement at the positive tumor by our contrast agent analyzed by Image J.
  • FIG. 4.6 Western Blot with PAbPEGCA1 (top) and NIR imaging (bottom) of different tissues of the tumor nice after MRI imaging.
  • FIG. 4.7 Immunohistochemistry (IHC) staining using the antibody PAbPGCA1 with tissue slides made from the tissue samples from the imaged mice, including HER2 tumors. Strongest staining was observed with liver and HER2 positive tumor tissue slides. The kidney slides also gave strong immunostaining. Interestingly, the areas near proximal tubes showed the strongest staining in the slides made from the kidney, indicating that the protein contrast agent was ready to be filtered through the kidney.
  • IHC Immunohistochemistry
  • FIG. 4.8 The binding of CAM-Affi with HER2 positive cells was measured by western blot.
  • FIG. 4.9 Immune staining of CaM-Affi treated breast cancer cells for skov-3 (Left, Her 2 positive) and MDA-MB-231 (right, Her2 negative).
  • FIG. 4.10 Immunostaining CA-Bom, CA-52I-Bom, CA at different time points for PC-3 and DU145 (GRPR high expression), and H441 (GRPR low expression).
  • FIG. 4.11 Near IR imaging of nude mice xenografted with DU-145 tumor (high expression of GRPR, left) and H441 tumor (low expression of GRPR, control, right) post injection of CA1.CD2-52Ibom-cy5.5-P40 26 hours via tail vein.
  • FIG. 4.12 NIR imaging (top) and NIR intensity (bottom) of CA1.CD2-52I-Bom-Cy5.5-P40 at different organs of the mice.
  • Embodiments of the present disclosure will employ, unless otherwise indicated, techniques of imaging, synthetic organic chemistry, biochemistry, biology, molecular biology, recombinant DNA techniques, pharmacology, and the like, which are within the skill of the art. Such techniques are explained fully in the literature.
  • a “contrast agent” is intended to include any agent that is physiologically tolerable and capable of providing enhanced contrast for magnetic resonance imaging.
  • a suitable contrast agent is preferably biocompatible, e.g., non-toxic, chemically stable, not absorbed by the body or reactive with a tissue, and eliminated from the body within a short time.
  • polymer means any compound that is made up of two or more monomeric units covalently bonded to each other, where the monomeric units may be the same or different, such that the polymer may be a homopolymer or a heteropolymer.
  • Representative polymers include peptides, polysaccharides, nucleic acids and the like, where the polymers may be naturally occurring or synthetic.
  • polypeptides includes proteins and fragments thereof. Polypeptides are disclosed herein as amino acid residue sequences. Those sequences are written left to right in the direction from the amino to the carboxy terminus. In accordance with standard nomenclature, amino acid residue sequences are denominated by either a three letter or a single letter code as indicated as follows: Alanine (Ala, A), Arginine (Arg, R), Asparagine (Asn, N), Aspartic Acid (Asp, D), Cysteine (Cys, C), Glutamine (Gln, Q), Glutamic Acid (Glu, E), Glycine (Gly, G), Histidine (His, H), Isoleucine (Ile, I), Leucine (Leu, L), Lysine (Lys, K), Methionine (Met, M), Phenylalanine (Phe, F), Proline (Pro, P), Serine (Ser, S), Threonine (Thr, T), Tryptophan
  • the protein can include non-standard and/or non-naturally occurring amino acids, as well as other amino acids that may be found in phosphorylated proteins in organisms such as, but not limited to, animals, plants, insects, protists, fungi, bacteria, algae, single-cell organisms, and the like.
  • the non-standard amino acids include, but are not limited to, selenocysteine, pyrrolysine, gamma-aminobutyric acid, carnitine, ornithine, citrulline, homocysteine, hydroxyproline, hydroxylysine, sarcosine, and the like.
  • the non-naturally occurring amino acids include, but are not limited to, trans-3-methylproline, 2,4-methanoproline, cis-4-hydroxyproline, trans-4-hydroxyproline, N-methyl-glycine, allo-threonine, methylthreonine, hydroxy-ethylcysteine, hydroxyethylhomocysteine, nitro-glutamine, homoglutamine, pipecolic acid, thiazolidine carboxylic acid, dehydroproline, 3- and 4-methylproline, 3,3-dimethylproline, tert-leucine, norvaline, 2-azaphenylalanine, 3-azaphenylalanine, 4-azaphenylalanine, and 4-fluorophenylalanine.
  • Variant refers to a polypeptide or polynucleotide or polymer that differs from a reference polypeptide or polynucleotide or polymer, but retains essential properties.
  • a typical variant of a polypeptide differs in amino acid sequence from another, reference polypeptide. Generally, differences are limited so that the sequences of the reference polypeptide and the variant are closely similar overall and, in many regions, identical.
  • a variant and reference polypeptide may differ in amino acid sequence by one or more modifications (e.g., substitutions, additions, and/or deletions).
  • a variant of a polypeptide includes conservatively modified variants.
  • a substituted or inserted amino acid residue may or may not be one encoded by the genetic code.
  • a variant of a polypeptide may be naturally occurring, such as an allelic variant, or it may be a variant that is not known to occur naturally.
  • a variant of a polypeptide may contain different modifications such as with PEGylation groups or the same type of groups with different sizes or lengths of the modifications.
  • Variant generated such as by modifying metal binding sites may have different metal binding properties and relaxivities and vivo peroperties.
  • the hydropathic index of amino acids can be considered.
  • the importance of the hydropathic amino acid index in conferring interactive biologic function on a polypeptide is generally understood in the art. It is known that certain amino acids can be substituted for other amino acids having a similar hydropathic index or score and still result in a polypeptide with similar biological activity. Each amino acid has been assigned a hydropathic index on the basis of its hydrophobicity and charge characteristics.
  • Those indices are: isoleucine (+4.5); valine (+4.2); leucine (+3.8); phenylalanine (+2.8); cysteine/cysteine (+2.5); methionine (+1.9); alanine (+1.8); glycine ( ⁇ 0.4); threonine ( ⁇ 0.7); serine ( ⁇ 0.8); tryptophan ( ⁇ 0.9); tyrosine ( ⁇ 1.3); proline ( ⁇ 1.6); histidine ( ⁇ 3.2); glutamate ( ⁇ 3.5); glutamine ( ⁇ 3.5); aspartate ( ⁇ 3.5); asparagine ( ⁇ 3.5); lysine ( ⁇ 3.9); and arginine ( ⁇ 4.5).
  • the relative hydropathic character of the amino acid determines the secondary structure of the resultant polypeptide, which in turn defines the interaction of the polypeptide with other molecules, such as enzymes, substrates, receptors, antibodies, antigens, and the like. It is known in the art that an amino acid can be substituted by another amino acid having a similar hydropathic index and still obtain a functionally equivalent polypeptide. In such changes, the substitution of amino acids whose hydropathic indices are within ⁇ 2 is preferred, those within ⁇ 1 are particularly preferred, and those within ⁇ 0.5 are even more particularly preferred.
  • hydrophilicity can also be made on the basis of hydrophilicity, particularly, where the biological functional equivalent polypeptide or peptide thereby created is intended for use in immunological embodiments.
  • the following hydrophilicity values have been assigned to amino acid residues: arginine (+3.0); lysine (+3.0); aspartate (+3.0 ⁇ 1); glutamate (+3.0 ⁇ 1); serine (+0.3); asparagine (+0.2); glutamine (+0.2); glycine (0); proline ( ⁇ 0.5 ⁇ 1); threonine ( ⁇ 0.4); alanine ( ⁇ 0.5); histidine ( ⁇ 0.5); cysteine ( ⁇ 1.0); methionine ( ⁇ 1.3); valine ( ⁇ 1.5); leucine ( ⁇ 1.8); isoleucine ( ⁇ 1.8); tyrosine ( ⁇ 2.3); phenylalanine ( ⁇ 2.5); tryptophan ( ⁇ 3.4).
  • an amino acid can be substituted for another having a similar hydrophilicity value and still obtain a biologically equivalent, and in particular, an immunologically equivalent polypeptide.
  • substitution of amino acids whose hydrophilicity values are within ⁇ 2 is preferred, those within ⁇ 1 are particularly preferred, and those within ⁇ 0.5 are even more particularly preferred.
  • amino acid substitutions are generally based on the relative similarity of the amino acid side-chain substituents, for example, their hydrophobicity, hydrophilicity, charge, size, and the like.
  • Exemplary substitutions that take various of the foregoing characteristics into consideration are well known to those of skill in the art and include (original residue: exemplary substitution): (Ala: Gly, Ser), (Arg: Lys), (Asn: Gln, His), (Asp: Glu, Cys, Ser), (Gln: Asn), (Glu: Asp), (Gly: Ala), (His: Asn, Gln), (Ile: Leu, Val), (Leu: Ile, Val), (Lys: Arg), (Met: Leu, Tyr), (Ser: Thr), (Thr: Ser), (Tip: Tyr), (Tyr: Trp, Phe), and (Val: Ile, Leu).
  • Embodiments of this disclosure thus contemplate functional or biological equivalents of a polypeptide as set forth above.
  • embodiments of the polypeptides can include variants having about 50%, 60%, 70%, 80%, 90%, and 95% sequence identity to the polypeptide of interest.
  • Identity is a relationship between two or more polypeptide sequences, as determined by comparing the sequences. In the art, “identity” also means the degree of sequence relatedness between polypeptides as determined by the match between strings of such sequences. “Identity” and “similarity” can be readily calculated by known methods, including, but not limited to, those described in (Computational Molecular Biology, Lesk, A. M., Ed., Oxford University Press, New York, 1988; Biocomputing: Informatics and Genome Projects, Smith, D. W., Ed., Academic Press, New York, 1993; Computer Analysis of Sequence Data, Part I, Griffin, A. M., and Griffin, H.
  • Preferred methods to determine identity are designed to give the largest match between the sequences tested. Methods to determine identity and similarity are codified in publicly available computer programs. The percent identity between two sequences can be determined by using analysis software (e.g., Sequence Analysis Software Package of the Genetics Computer Group, Madison Wis.) that incorporates the Needelman and Wunsch, (J. Mol. Biol., 48: 443-453, 1970) algorithm (e.g., NBLAST and XBLAST). The default parameters are used to determine the identity of the polypeptides of the present disclosure.
  • a polypeptide sequence may be identical to the reference sequence, that is 100% identical, or it may include up to a certain integer number of amino acid alterations as compared to the reference sequence such that the % identity is less than 100%.
  • Such alterations are selected from: at least one amino acid deletion, substitution, including conservative and non-conservative substitution, or insertion, and wherein said alterations may occur at the amino- or carboxy-terminal positions of the reference polypeptide sequence or anywhere between those terminal positions, interspersed either individually among the amino acids in the reference sequence or in one or more contiguous groups within the reference sequence.
  • the number of amino acid alterations for a given % identity is determined by multiplying the total number of amino acids in the reference polypeptide by the numerical percent of the respective percent identity (divided by 100) and then subtracting that product from said total number of amino acids in the reference polypeptide.
  • Non-naturally occurring amino acids include, without limitation, trans-3-methylproline, 2,4-methanoproline, cis-4-hydroxyproline, trans-4-hydroxyproline, N-methyl-glycine, allo-threonine, methylthreonine, hydroxy-ethylcysteine, hydroxyethylhomocysteine, nitro-glutamine, homoglutamine, pipecolic acid, thiazolidine carboxylic acid, dehydroproline, 3- and 4-methylproline, 3,3-dimethylproline, tert-leucine, norvaline, 2-azaphenyl-alanine, 3-azaphenylalanine, 4-azaphenylalanine, and 4-fluorophenylalanine.
  • coli cells are cultured in the absence of a natural amino acid that is to be replaced (e.g., phenylalanine) and in the presence of the desired non-naturally occurring amino acid(s) (e.g., 2-azaphenylalanine, 3-azaphenylalanine, 4-azaphenylalanine, or 4-fluorophenylalanine).
  • the non-naturally occurring amino acid is incorporated into the protein in place of its natural counterpart.
  • Naturally occurring amino acid residues can be converted to non-naturally occurring species by in vitro chemical modification. Chemical modification can be combined with site-directed mutagenesis to further expand the range of substitutions (Wynn, et al., Protein Sci., 2: 395-403, 1993).
  • polynucleotide generally refers to any polyribonucleotide or polydeoxyribonucleotide, which may be unmodified RNA or DNA or modified RNA or DNA.
  • polynucleotides as used herein refers to, among others, single- and double-stranded DNA, DNA that is a mixture of single- and double-stranded regions, single- and double-stranded RNA, and RNA that is mixture of single- and double-stranded regions, hybrid molecules comprising DNA and RNA that may be single-stranded or, more typically, double-stranded or a mixture of single- and double-stranded regions.
  • Polynucleotide encompasses the terms “nucleic acid,” “nucleic acid sequence,” or “oligonucleotide” as defined above.
  • polynucleotide as used herein refers to triple-stranded regions comprising RNA or DNA or both RNA and DNA.
  • the strands in such regions may be from the same molecule or from different molecules.
  • the regions may include all of one or more of the molecules, but more typically involve only a region of some of the molecules.
  • One of the molecules of a triple-helical region often is an oligonucleotide.
  • polynucleotide includes DNAs or RNAs as described above that contain one or more modified bases.
  • DNAs or RNAs with backbones modified for stability or for other reasons are “polynucleotides” as that term is intended herein.
  • DNAs or RNAs comprising unusual bases, such as inosine, or modified bases, such as tritylated bases, to name just two examples are polynucleotides as the term is used herein.
  • polynucleotide as it is employed herein embraces such chemically, enzymatically or metabolically modified forms of polynucleotides, as well as the chemical forms of DNA and RNA characteristic of viruses and cells, including simple and complex cells, inter alias.
  • a polynucleotide sequence of the present disclosure may be identical to the reference sequence, that is be 100% identical, or it may include up to a certain integer number of nucleotide alterations as compared to the reference sequence.
  • Such alterations are selected from the group including at least one nucleotide deletion, substitution, including transition and transversion, or insertion, and wherein said alterations may occur at the 5′ or 3′ terminal positions of the reference nucleotide sequence or anywhere between those terminal positions, interspersed either individually among the nucleotides in the reference sequence or in one or more contiguous groups within the reference sequence.
  • the number of nucleotide alterations is determined by multiplying the total number of nucleotides in the reference nucleotide by the numerical percent of the respective percent identity (divided by 100) and subtracting that product from said total number of nucleotides in the reference nucleotide. Alterations of a polynucleotide sequence encoding the polypeptide may alter the polypeptide encoded by the polynucleotide following such alterations.
  • Codon means a specific triplet of mononucleotides in the DNA chain. Codons correspond to specific amino acids (as defined by the transfer RNAs) or to start and stop of translation by the ribosome.
  • degenerate nucleotide sequence denotes a sequence of nucleotides that includes one or more degenerate codons (as compared to a reference polynucleotide molecule that encodes a polypeptide).
  • Degenerate codons contain different triplets of nucleotides, but encode the same amino acid residue (e.g., GAU and GAC triplets each encode Asp).
  • antibody is used to refer both to a homogenous molecular entity, or a mixture such as a serum product made up of a plurality of different molecular entities.
  • Monoclonal or polyclonal antibodies, which specifically react with the virosomes of the present disclosure, may be made by methods known in the art. (e.g., Harlow and Lane (1988) Antibodies: A Laboratory Manual , Cold Spring Harbor Laboratories; Goding (1986) Monoclonal Antibodies: Principles and Practice, 2d ed., Academic Press, New York; and Ausubel et al. (1987)).
  • recombinant immunoglobulin may be produced by methods known in the art, including but not limited to, the methods described in U.S. Pat. No. 4,816,567, which is hereby incorporated by reference herein.
  • Affibody® ligands (U.S. Pat. No. 5,831,012, which is incorporated herein by reference) are highly specific affinity proteins that may be designed and used like aptamers.
  • Affibodies may be produced or purchased from commercial sources (Affibody AB, Bromma, Sweden). Aptamers and affibodies may be used in combination with antibodies to increase the functional avidity of translucent or non-translucent solid matrices for probe molecule binding. Increased binding in turn results in an increased signal strength, greater signal-to-noise ratio, more reproducible target molecule detection and greater sensitivity of detection.
  • Aptamers must also be differentiated from the naturally occurring nucleic acid sequences that bind to certain proteins. These latter sequences generally are naturally occurring sequences embedded within the genome of the organism that bind to a specialized sub-group of proteins or polypeptides, or their derivatives, that are involved in the transcription, translation, and transportation of naturally occurring nucleic acids, i.e., protein-binding nucleic acids. Aptamers on the other hand are short, isolated, non-naturally occurring nucleic acid molecules. While aptamers can be identified that bind nucleic acid-binding proteins, in most cases such aptamers have little or no sequence identity to the sequences recognized by the nucleic acid-binding proteins in nature.
  • aptamers can be selected to bind virtually any protein (not just nucleic acid-binding proteins) as well as almost any target of interest including small molecules, carbohydrates, peptides, etc.
  • a naturally occurring nucleic acid sequence to which it binds does not exist.
  • nucleic acid-binding proteins such sequences will differ from aptamers as a result of the relatively low binding affinity used in nature as compared to tightly binding aptamers.
  • Aptamers are capable of specifically binding to selected targets and modulating the target's activity or binding interactions, e.g., through binding, aptamers may block their target's ability to function.
  • the functional property of specific binding to a target is an inherent property of an aptamer.
  • a typical aptamer is 6-35 kDa in size (20-100 nucleotides), binds its target with micromolar to sub-nanomolar affinity, and may discriminate against closely related targets (e.g., aptamers may selectively bind related proteins from the same gene family).
  • Aptamers are capable of using intermolecular interactions such as hydrogen bonding, electrostatic complementarities, hydrophobic contacts, and steric exclusion to bind with a specific target.
  • aptamers also employ boronic acid-Lewis base/nucleophile (such as hydroxyl groups, diols, and amino groups) interactions for binding. Aptamers have a number of desirable characteristics for use as therapeutics and diagnostics including high specificity and affinity, low immunogenicity, biological efficacy, and excellent pharmacokinetic properties.
  • PEGylation means and refers to modifying a polymer (e.g., a protein) by covalently attaching polyethylene glycol (PEG) to the polymer, with “PEGylated” referring to a polymer having a PEG attached.
  • PEGylation methods see, for example, the Nektar Advanced PEGylation Catalogs 2004 and 2005-2006, as well as the references cited therein.
  • PEGYlation can be achieved by non-specific interaction with functional group of polypeptide chain such as via amino group or specific interaction at certain location of the macromolecules such as amino terminal or at the Cys residues.
  • biomarker or “biomarker probe” are used to refer to a substance used as an indicator of a biologic state. It is a characteristic that is objectively measured and evaluated as an indicator of normal biologic processes, pathogenic processes, and/or pharmacologic responses to a therapeutic intervention.
  • disease marker is used to refer to substances, such as proteins, bio-chemicals, nucleic acids, carbohydrates, or enzymes, produced by disease cells or by the body in response to disease cells during disease development and progression. These substances are indicative of a particular disease process.
  • treatment As used herein, the terms “treatment”, “treating”, and “treat” are defined as acting upon a disease, disorder, or condition with an agent to reduce or ameliorate the pharmacologic and/or physiologic effects of the disease, disorder, or condition and/or its symptoms.
  • Treatment covers any treatment of a disease in a host (e.g., a mammal, typically a human or non-human animal of veterinary interest), and includes: (a) reducing the risk of occurrence of the disease in a subject determined to be predisposed to the disease but not yet diagnosed as infected with the disease (b) impeding the development of the disease, and (c) relieving the disease, i.e., causing regression of the disease and/or relieving one or more disease symptoms. “Treatment” is also meant to encompass delivery of a contrast agent including a compound to provide a pharmacologic effect, even in the absence of a disease or condition.
  • treatment encompasses delivery of a disease or pathogen compound via the contrast agent that provides for enhanced or desirable effects in the subject (e.g., reduction of pathogen load, reduction of disease symptoms, etc.).
  • prophylactically treat or “prophylactically treating” refers to completely or partially preventing a disease or symptom thereof and/or may be therapeutic in terms of a partial or complete cure for a disease and/or adverse effect attributable to the disease.
  • unit dosage form refers to physically discrete units suitable as unitary dosages for human and/or animal subjects, each unit containing a predetermined quantity of a contrast agent calculated in an amount sufficient to produce the desired effect in association with a pharmaceutically acceptable diluent, carrier or vehicle.
  • the specifications for unit dosage forms depend on the particular compound employed, the route and frequency of administration, the effect to be achieved, and the pharmacodynamics associated with each compound in the host.
  • a “pharmaceutically acceptable excipient,” “pharmaceutically acceptable diluent,” “pharmaceutically acceptable carrier,” or “pharmaceutically acceptable adjuvant” means an excipient, diluent, carrier, and/or adjuvant that are useful in preparing a pharmaceutical composition that are generally safe, non-toxic and neither biologically nor otherwise undesirable, and include an excipient, diluent, carrier, and adjuvant that are acceptable for veterinary use and/or human pharmaceutical use.
  • “A pharmaceutically acceptable excipient, diluent, carrier and/or adjuvant” as used in the specification and claims includes one or more such excipients, diluents, carriers, and adjuvants.
  • a “pharmaceutical composition” is meant to encompass a contrast agent suitable for administration to a subject, such as a mammal, especially a human.
  • a “pharmaceutical composition” is sterile, and preferably free of contaminants that are capable of eliciting an undesirable response within the subject (e.g., the compound(s) in the pharmaceutical composition is pharmaceutical grade).
  • Pharmaceutical compositions can be designed for administration to subjects or patients in need thereof via a number of different routes of administration including oral, intravenous, buccal, rectal, parenteral, intraperitoneal, intradermal, intracheal, intramuscular, subcutaneous, inhalational and the like.
  • the terms “therapeutically effective amount” and “an effective amount” are used interchangeably herein and refer to that amount of a contrast agent being administered that is sufficient to effect the intended application.
  • the effective amount of the contrast agent includes enough so that the disease, for example, in the host can be imaged, studied, diagnosed, or the like.
  • an effective amount of a contrast agent including a compound will relieve to some extent one or more of the symptoms of the disease being treated, and/or that amount that will prevent, to some extent, one or more of the symptoms of the disease that the host being treated has or is at risk of developing.
  • the therapeutically effective amount may vary depending upon the intended application (in vitro or in vivo), or the subject and disease condition being treated, e.g., the weight and age of the subject, the severity of the disease condition, the manner of administration and the like, which can readily be determined by one of ordinary skill in the art.
  • the term also applies to a dose that will induce a particular response in target cells.
  • the specific dose will vary depending on the particular compounds chosen, the dosing regimen to be followed, whether it is administered in combination with other compounds, timing of administration, the tissue to which it is administered, and the physical delivery system in which it is carried.
  • the term “host,” “subject,” “patient,” or “organism” includes humans and mammals (e.g., mice, rats, pigs, cats, dogs, and horses). Typical hosts to which compounds of the present disclosure may be administered will be mammals, particularly primates, especially humans. For veterinary applications, a wide variety of subjects will be suitable, e.g., livestock such as cattle, sheep, goats, cows, swine, and the like; poultry such as chickens, ducks, geese, turkeys, and the like; and domesticated animals particularly pets such as dogs and cats.
  • livestock such as cattle, sheep, goats, cows, swine, and the like
  • poultry such as chickens, ducks, geese, turkeys, and the like
  • domesticated animals particularly pets such as dogs and cats.
  • living host refers to a host noted above or another organism that is alive.
  • living host refers to the entire host or organism and not just a part excised (e.g., a liver or other organ) from the living host.
  • Cancer as used herein, shall be given its ordinary meaning, as a general term for diseases in which abnormal cells divide without control.
  • cancer refers to angiogenesis related cancer. Cancer cells can invade nearby tissues and can spread through the bloodstream and lymphatic system to other parts of the body.
  • carcinoma is cancer that begins in the skin or in tissues that line or cover internal organs.
  • Sarcoma is cancer that begins in bone, cartilage, fat, muscle, blood vessels, or other connective or supportive tissue.
  • Leukemia is cancer that starts in blood-forming tissue such as the bone marrow, and causes large numbers of abnormal blood cells to be produced and enter the bloodstream.
  • Lymphoma is cancer that begins in the cells of the immune system.
  • a tumor When normal cells lose their ability to behave as a specified, controlled and coordinated unit, a tumor is formed.
  • a solid tumor is an abnormal mass of tissue that usually does not contain cysts or liquid areas (some brain tumors do have cysts and central necrotic areas filled with liquid). A single tumor may even have different populations of cells within it, with differing processes that have gone awry.
  • Solid tumors may be benign (not cancerous), or malignant (cancerous). Different types of solid tumors are named for the type of cells that form them. Examples of solid tumors are sarcomas, carcinomas, and lymphomas. Leukemias (cancers of the blood) generally do not form solid tumors.
  • Representative cancers include, but are not limited to, bladder cancer, breast cancer, colorectal cancer, endometrial cancer, head and neck cancer, lung cancer, lymphoma, melanoma, non-small-cell lung cancer, ovarian cancer, prostate cancer, testicular cancer, uterine cancer, cervical cancer, thyroid cancer, gastric cancer, brain stem glioma, cerebellar astrocytoma, cerebral astrocytoma, glioblastoma, ependymoma, Ewing's sarcoma family of tumors, germ cell tumor, extracranial cancer, Hodgkin's disease, leukemia, acute lymphoblastic leukemia, acute myeloid leukemia, liver cancer, medulloblastoma, neuroblastoma, brain tumors generally, non-Hodgkin's lymphoma, osteosarcoma, malignant fibrous histiocytoma of bone, retinoblastoma, rhabdomyosarcom
  • a tumor can be classified as malignant or benign. In both cases, there is an abnormal aggregation and proliferation of cells. In the case of a malignant tumor, these cells behave more aggressively, acquiring properties of increased invasiveness. Ultimately, the tumor cells may even gain the ability to break away from the microscopic environment in which they originated, spread to another area of the body (with a very different environment, not normally conducive to their growth), and continue their rapid growth and division in this new location. This is called metastasis. Once malignant cells have metastasized, achieving a cure is more difficult.
  • Benign tumors have less of a tendency to invade and are less likely to metastasize. Brain tumors spread extensively within the brain but do not usually metastasize outside the brain. Gliomas are very invasive inside the brain, even crossing hemispheres. They do divide in an uncontrolled manner, though. Depending on their location, they can be just as life threatening as malignant lesions. An example of this would be a benign tumor in the brain, which can grow and occupy space within the skull, leading to increased pressure on the brain.
  • precancerous cells cancer cells, cancer, and tumors may be used interchangeably in the disclosure.
  • embodiments of the present disclosure in one aspect, relate to contrast agents, compositions including contrast agents, methods of making contrast agents, methods of imaging, methods of diagnosing, methods of studying, and the like. More particularly, embodiments of the contrast agents include magnetic resonance imaging contrast agents that accumulate in tissue and can be used to determine the presence and/or location of a target.
  • contrast agents of the present disclosure can include targeting agents to target cells or tissue (e.g., cancer).
  • Embodiments of the present disclosure can be tuned to have properties for diagnostic imaging.
  • the contrast agent includes a metal ion interacting (e.g., bonding with or chelating with) with the metal ion binding site.
  • a contrast agent can include two metal ions interacting (e.g., bonding with or chelating with) with two metal ion binding sites.
  • the metal ion binding site may be developed by a design approach or by a grafting approach. After the site has been developed, the site or sites are operatively integrated into the select areas of the scaffold polymer.
  • the contrast agent is stable in a physiological environment.
  • physiological environment can be described as cell, cellular conditions, tissues, organs, and vertebrate/invertebrates, animal/human or buffer conditions (e.g., pH of about 6-8 and a temperature of about 5-45° C.) mimic closely to the cellular, or in vivo conditions.
  • stable in reference to “physiological environment” means that the contrast agent is able to provide contrast capability and remain intact.
  • the phrase “stable in a physiological environment” refers to the contrast agent including at least one metal ion and the binding of the metal ion causes no changes or substantially no changes (e.g., less than 50%) to the protein (scaffold protein) conformation or to the binding affinity of the tailored metal ion binding site under clinical conditions (physiological environment) that would cause premature release of the metal ion, and that the contrast agent functions as a contrast agent as described herein.
  • the scaffold polymer of the contrast agent includes polyethylene glycerol compounds (PEG) attached to the polymer.
  • PEG polyethylene glycerol compounds
  • the PEGs can be attached (e.g., bonded) to the polymer via an amino acid residue such as lysine (Lys), glutamic acid (Glu), aspartic acid (Asp), cysteine (Cys), and/or carboxyl/amino terminals.
  • the position of the amino acids on the polymer can be selected to position the PEGs so that the PEGs do not substantially interfere (e.g., decrease metal binding affinity more than 20%) with or interfere with the metal ion binding sites ability to interact with the metal ion of interest or the conformation of the polymer.
  • the PEGs are attached to one or more Lys residues since the position of the Lys residues on the polymer is such that the PEGs do not substantially interfere with or interfere with the metal ion binding site ability to interact with the metal ion of interest or the conformation of the polymer.
  • reference to “contrast agent” refers to a contrast agent that includes PEGs.
  • embodiments of the present disclosure include contrast agents that include PEGs and contrast agents that do not include PEGs. Additional details regarding PEGs are described herein.
  • Embodiments of the present disclosure provide for PEGylated contrast agents, where the PEGylation increases the blood circulation time of the contrast agent in CD-1 mice.
  • PEGylation of the contrast agent increased the solubility of the contrast agent by more than two-fold, three-fold, four-fold, five-fold, six-fold, seven-fold, eight-fold, nine-fold, ten-fold, or more relative to the un-PEGylated contrast agent.
  • PEGylation of the contrast agent further increased the in vitro of one or both R1 and R2 relaxivities of the contrast agents by about 10%, 25%, 50%, 75%, 100%, or 2-3 fold or more, relative to the un-PEGylated contrast agent.
  • the increase in molecular size due to the PEGylation and the addition of a hydration layer due to water retention by Poly-PEG chain on protein surface may be the reasons for the increases in the relaxivities.
  • Embodiments of this disclosure include contrast agents capable of enhancing image contrast by affecting water molecule proton relaxation rates. Such contrast agents are effective for magnetic resonance imaging, in part, because the water proton relaxation rate in the target tissue is affected differently from the relaxation rate of the water protons in the surrounding tissue.
  • the contrast agents are paramagnetic species, which form complexes with metal ions, so to alter the relaxation rates of adjacent nuclei.
  • the scaffold polymer (referred to as a “protein” or “peptide” hereinafter) for MRI applications are a protein that will host the tailored metal ion binding sites and has the following characteristics:
  • a rotational correlation time optimized for the magnetic field e.g., around 100 milliseconds in a magnetic field of 1.3 to 3T
  • higher magnetic field application can demand a host protein with a larger molecular weight
  • the contrast agent for use in MRI applications can include a scaffold protein (referred to as a “protein”, “polymer”, or “peptide”) that includes a natural metal binding protein or a fragment/domain of natural metal binding proteins either with metal binding sites modified by at least one amino acid or protein modification.
  • a scaffold protein referred to as a “protein”, “polymer”, or “peptide” that includes a natural metal binding protein or a fragment/domain of natural metal binding proteins either with metal binding sites modified by at least one amino acid or protein modification.
  • Properties of the scaffold protein also may include water solubility, low interaction with the other cellular metal ions and low toxicity. While all these properties are not required, the optimal properties of the scaffold protein can depend on the specific parameters of the imaging application.
  • the scaffold protein has a three-dimensional structure or an amino sequence with some homology to the proteins whose structures have been solved, at least in part. Specifically, the scaffold protein is screened to determine whether it can tolerate the integration of various binding sites without excessive denaturation. For example, the integration of metal ion binding sites into the scaffold protein should not denature or unfold the protein. Thus, the metal ion binding site should not be placed by mutating a hydrophobic core or in a position that results in substantial structural perturbation. This can be examined by sequence alignment of proteins in the same family. In an embodiment, the amino acids that have an essential role in folding of the structure or the function will be conserved among different species of this same type of the protein.
  • metal ion binding sites are placed into a scaffold protein such that the metal can be tumbled together with the protein. It is better to find a location that is not so flexible or the same flexibility as the protein body so as to match the correction time. In an embodiment, it is preferred to design or create the binding pocket in the protein. Although insertion could work, it is preferable to do so in a relatively not so flexible region.
  • the protein can be checked by looking at the B factor (temperature factor for X-ray) or S2 factor (dynamic flexibility factor for NMR) of the pdb (protein data bank) file of the structure.
  • more than one metal binding site may be integrated into a scaffold protein.
  • the inclusion of more than one binding site improves the sensitivity of the contrast agent.
  • the site could have different affinities, but should still have strong enough affinity for the selected metal so to avoid competition with physiological metal ions. Both metal ions should be embedded into the host protein with preferred rotational correlation times and water exchange rates to provide MRI contrast with an increased sensitivity.
  • the contrast agent can have a high affinity to and can preferentially select a particular metal ion (e.g., Gd 3+ , Mn 2+ , or Fe 3+ ).
  • exemplary contrast agents showed a dissociation constant K d less than 10 12 [M] for Gd 3+ in an environment having physiological metal ions and prevented those metal ions from precipitation under physiological conditions.
  • the present disclosure may be used to create contrast agents having optimal selectivity for a specific metal ion.
  • Embodiments of the present disclosure can provide a new mechanism to increase the relaxivity of contrast agents. This is accomplished by designing the metal ion binding sites, e.g., Gd 3+ , in proteins, which can eliminate the mobility and flexibility of the chelating moiety associated with currently available contrast agents. High proton relaxivity by contrast agents can further enhance images.
  • the metal ion binding sites e.g., Gd 3+
  • An advantage of the present disclosure is that it provides contrast agents that can preferentially chelate a specific metal ion.
  • a preferred contrast agent having Gd 3+ binding site(s) will preferentially chelate Gd 3+ over other metal ions, such as Mg 2+ or Ca 2+ .
  • the ability to preferentially chelate a specific metal ion can improve the specificity of a contrast agent and reduces the cytotoxicity of the contrast agent.
  • the contrast agents include PEGs attached to the protein. Inclusion of the PEGs in the contrast agent increases blood circulation time, increases the solubility of the contrast agent in a physiological system, and/or increases R1 and R2 relaxivities, relative to un-PEGylated contrast agents.
  • the PEGs are bonded to the protein via an amino acid residue such as lysine (Lys), glutamic acid (Glu), aspartic acid (Asp), cysteine (Cys), carboxyl/amino terminals, or combinations thereof.
  • the position of the amino acids on the polymer should position the PEGs so that the PEGs do not substantially interfere with or interfere with the metal ion binding site ability to interact with the metal ion of interest or the conformation of the polymer.
  • a fusion protein/peptide/polymer or a non-degradable particle moiety can be added to the protein contrast agent with a linker to tune the correlation time for optimal contrast sensitivity, targeting (e.g., subcellular, cellular, tissue and organ selectivity), biodistribution (e.g., affiibody against to Her-2 was fused to CA1 as a targeted contrast agent to breast cancer), and/or bioelimination (e.g., using proteins with molecular weight less than 60 KDa).
  • targeting e.g., subcellular, cellular, tissue and organ selectivity
  • biodistribution e.g., affiibody against to Her-2 was fused to CA1 as a targeted contrast agent to breast cancer
  • bioelimination e.g., using proteins with molecular weight less than 60 KDa
  • Scaffold proteins suitable with the present disclosure include proteins or organic polymers containing amino acids.
  • the scaffold proteins can be modified.
  • the scaffold proteins are inclusive of both natural amino acids and unnatural amino acids (e.g., beta-alanine, phenylglycine, and homoarginine, Gamma-carboxyglutamate (Gla)).
  • the amino acids are alpha-amino acids, which can be either of the L-optical isomer or the D-optical isomer.
  • the amino acids are D-optical isomers, as such isomers are less subject to proteolytic degradation.
  • Such amino acids can be commonly encountered amino acids that are not gene-encoded, although preferred amino acids are those that are encodable.
  • a Near-IR functional group e.g., Cy5.5, Cy7, Alexflour, and indocyanine green
  • a targeting agent for Near-IR detection is covalently bound to the scaffold protein, a PEG, and/or a targeting agent.
  • the scaffold proteins should include one or more amino acid residues (e.g., Lys, Glu, Asp, Cys, or combinations thereof) able to bond with the PEGs or otherwise modified.
  • the position of the amino acids on the protein should position the PEGs so that the PEGs do not substantially interfere with or interfere with the metal ion binding site ability to interact with the metal ion of interest or the conformation of the polymer.
  • scaffold proteins may be used according to the disclosure, but in general they will be proteins, and organic polymers. More specifically, suitable scaffold proteins can be selected properties suitable for diagnostic applications.
  • the scaffold protein for use with this disclosure may be of unitary construction (a particulate, a polychelant or a dendrimeric polymer). Scaffold proteins suitable with this disclosure may be selected without undue experimentation.
  • Embodiments of the present disclosure can include proteins such as CD2 proteins (a cell adhesion protein) that exhibit high stability against proteolysis, thermal conditions (Tm 67° C.), pH (2-10), and salt (0-4 M NaCl) denaturation.
  • CD2 proteins can be suitable with this disclosure because such proteins are stable in physiological environments, have a topology suitable for the integration of at least one or multiple metal ion chelating sites, and typically have a relaxivity greater than 10 mM ⁇ 1 s ⁇ 1 (some of them up to about 50 mM ⁇ 1 s ⁇ 1 ).
  • CD2 proteins can tolerate multiple surface mutations without unfolding the protein.
  • the CD2 proteins can be used as a host protein to design calcium binding sites. Examples using CD2 are described herein.
  • Fluorescent proteins are another class of preferred scaffold protein for this disclosure, as these proteins are stable in a physiological environment against proteolytic degradation and pH denaturation (pH 5-10).
  • Such fluorescent proteins include an array of fluorescent proteins including those related to Aequorea . Suitable fluorescent proteins should have a useful excitation and emission spectra and may have been engineered from naturally occurring Aequorea victoria green fluorescent proteins (GFPs).
  • GFPs green fluorescent proteins
  • modified GFPs may have modified nucleic acid and protein sequences and may include elements from other proteins.
  • the cDNA of GFPs may be concatenated with those encoding many other proteins—the resulting chimerics are often fluorescent and retain the biochemical features of the partner proteins.
  • Such proteins also are included in the disclosure.
  • contrast agents constructed from such proteins can be multi-functional probes.
  • the contrast agent constructed from fluorescent proteins can be screened using both fluorescence and MR imaging. This can be advantageous as such properties equip the contrast agent with both the fluorescence needed for fluorescence detection methods and sensitivity needed for the deep tissue detection from MRI.
  • Such contrast agents are multifunctional contrast agents.
  • scaffold proteins are able to tolerate the addition of the metal ion binding site without substantial disruption to its structure.
  • metal binding site such as calcium binding sites as scaffold protein proteins.
  • These natural metal binding proteins such as calmodulin, calbindin D9K, troponin C, and parvalbumin, can be engineered to bind paramagnetic metal ions with very strong metal binding affinity thus are capable of enhancing image contrast by affecting water molecule proton relaxation rates.
  • Embodiments of scaffold protein sequences that can be included in the contrast agent are provided that include the unmodified scaffold proteins and modified scaffold proteins (insertions and/or deletions) for a variety of illustrative scaffold proteins that include metal ion binding sites.
  • the scaffold protein sequences include one or more possible locations for attachment of PEGs, mutation sites, C-terminal sites for pegylation or conjugation of moieties (e.g., fluorescent dyes), and the like.
  • embodiments of the present disclosure include contrast agents where PEGs are attached to the protein via one or more amino acid residues such as Lys, Glu, Asp, Cys, carboxyl/amino terminals, or combinations thereof.
  • the PEGs are attached to amino acid residues so that the PEGs do not substantially interfere with or interfere with the metal ion binding site ability to interact with the metal ion of interest or the conformation of the polymer.
  • the PEGs can be attached to the amino acid residues through PEGylation processes known in the art. The PEGylation may, for example, be performed at a pH of about 7.5 to 9 or about 8 to 8.5.
  • the PEGs can be linear PEGs, multi-arm PEGs, branched PEGs, and combinations thereof.
  • the molecular weight of the PEGs can be about 1 kDa to 100 kDa, about 1 kDa to 50 kDa, about 1 kDa to 40 kDa, about 1 kDa to 30 kDa, about 1 kDa to 20 kDa, about 1 kDa to 12 kDa, about 1 kDa to 10 kDa, or about 1 kDa to 8 kDa. It should be noted that the molecular weight can be any integer within any of the values mentioned above.
  • the word “about” indicates an approximate average molecular weight and reflects the fact that there will normally be a certain molecular weight distribution in a given polymer preparation.
  • 1 to 10 PEGs can be attached to the scaffold protein.
  • 2 to 6 PEGs can be attached to the scaffold protein.
  • 2 to 4 PEGs can be attached to the scaffold protein.
  • the PEGs can have additional functional groups to allow us to further modify the contrast agent by adding other moieties such as signal peptides (such as GRP signal peptide for targeting to prostate cancer).
  • signal peptides such as GRP signal peptide for targeting to prostate cancer.
  • a targeting agent can be attached (e.g., directly or indirectly) to the scaffold polymer or the PEG, where the targeting agent has an affinity for a target (e.g., a cell, a tissue, a protein, an antibody, an antigen, and the like).
  • the targeting agent can include, but is not limited to, polypeptides (e.g., proteins such as, but not limited to, antibodies (monoclonal or polyclonal)), antigens, nucleic acids (both monomeric and oligomeric), polysaccharides, sugars, fatty acids, steroids, purines, pyrimidines, ligands, or combinations thereof, where the targeting agent binds or otherwise interacts with the target.
  • the targeting agent specifically interacts with a specific type of target or specific target and substantially (e.g., 90%, 95%, 99% or more specificity to the target or type of target) or completely excludes other targets.
  • the targeting agent has an affinity for one or more targets.
  • the targeting agent can include: a biomarker probe, a precancerous targeting agent, a cancer targeting agent, a tumor targeting agent, and a probe or agent that targets at least two of a biomarker, a precancerous cell, a cancer cell, and a tumor.
  • the targeting agent can be linked, directly or indirectly, using a stable physical, biological, biochemical, and/or chemical association.
  • the targeting agent can be independently linked to the scaffold polymer or the PEG using, but not limited to, a covalent link, a non-covalent link, an ionic link, a chelated link, as well as being linked through interactions such as, but not limited to, hydrophobic interactions, hydrophilic interactions, charge-charge interactions, ⁇ -stacking interactions, combinations thereof, and like interactions.
  • the targeting agent can include, but is not limited to, (gastrin release peptide (GRP) that can bind to specific types of cancer receptors, i.e. GRP receptors, and, RGD peptides (Arg-Gly-Asp) (corresponding to integrin ⁇ v ⁇ 3 target).
  • GRP gastrin release peptide
  • RGD Arg-Gly-Asp
  • molecules that can be targets include, but are not limited to, vascular receptors (e.g., Vascular endothelial growth factor receptor (VEGF-R)), extracellular matrix proteins (e.g., proteases, MMP, thrombin), cell membrane receptors (e.g., epidermal growth factor receptor (EGFR) (e.g., HER2)), intracellular proteins, enzymes (e.g., caspases and PSA), serum proteins (e.g., albumin), and the like.
  • vascular receptors e.g., Vascular endothelial growth factor receptor (VEGF-R)
  • extracellular matrix proteins e.g., proteases, MMP, thrombin
  • cell membrane receptors e.g., epidermal growth factor receptor (EGFR) (e.g., HER2)
  • intracellular proteins e.g., enzymes (e.g., caspases and PSA), serum proteins (e.g., albumin), and the like.
  • An engineered metal binding site can be created by a combination of more than one above mentioned methods.
  • the computational design approach focuses on designing a metal ion binding site de novo. This design approach focuses on using an algorithm to construct and engineer an optimal binding site. Preferably, the computation design approach is used to create optimal binding sites by, e.g., varying the coordination geometry of the site, the water number in the coordination shells, the ligand types, and the charges.
  • the computational design approach comprises the following steps:
  • the metal ion binding site may be incorporated into a scaffold protein, e.g., a fluorescent or CD2 protein. Further, such a method may be used to alter metal ion binding properties of proteins and generate new materials with various ion binding affinities.
  • the method involves searching and accessing public and or private databases for preferred components of a metal ion binding site.
  • databases that may be searched for the criteria or components may include public domain banks (e.g., NBCI or PubMed) or knowledge banks such as protein modeling structure data banks (e.g., Cambridge or RCSB Protein Data Bank Data Bank and BioMagResBank database) or data bank.
  • the database could include structural data from metal ion binding proteins whose structures have been characterized previously.
  • One of ordinary skill in the art can identify databases and sources of material for databases suitable with this disclosure. Use of a computer obviously would greatly speed up the searching and is preferred.
  • These databases may be used to provide structural analysis of one to several thousand different small molecules or metal ions that bind to a protein.
  • Such analysis may include local coordination properties, types of residues or atoms commonly used to bind a desired metal ion, chemical features (e.g., pKa or changes), the number of charged residues on a site, and the range or deviation of the known binding sites.
  • Further, such analysis may include the environment, such as types of atoms, residues, hydrophobicity, solvent accessibility, shapes of the metal binding sites, electrostatic potentials, and the dynamic properties (e.g., B-factors or the order factors of the proteins) of the binding sites.
  • Such analysis also may include whether a binding site for a particular metal ion is a continuous or discontinuous binding site.
  • one or more suitable metal ion binding sites may be generated based on rational factors.
  • different search algorithms may be used to generate potential metal ion binding sites based on other key features in addition to, for example, the geometric descriptors. These key features include the properties of the original residues in the scaffold protein, ligand positions that are essential to protein folding, the number of the charged residues and their arrangement and number of water molecules in the coordination shell. The hydrogen bond network and the electrostatic interactions with the designed ligand residues also can be evaluated.
  • the protein environments of metal ion binding sites can be analyzed according to solvent accessibility, charge distribution, backbone flexibility, and properties of scaffold proteins. Thus, one of ordinary skill in the art may rationally select a binding site based on desired parameters.
  • a site may be tailored using two complementary approaches of computational design and grafting (see below).
  • the computational design approach includes modifying the metal ion binding site by modifying residues in the scaffold of the metal ion binding site.
  • a geometric description of the ligands around a metal ion, a three-dimensional structure of the backbone of proteins, and a library of side-chain rotamers of amino acids (or atoms from the main chain) can identify a set of potential metal-binding sites using a computer.
  • key ligand residues are carefully placed in the amino acid sequence to form the metal (metal ion) binding pocket. This binding pocket can be created automatically by the computer algorithm according to the coordination description and the user's preferred affinity.
  • the created potential metal ion binding sites can be optimized and tuned to specification.
  • a backbone structure of the metal ion binding site with different degrees of flexibility may be used according to the need or the flexibility of the metal ion binding site.
  • the designed metal ion binding sites are further filtered and scored based on the local factors, which may include the shape of the metal ion binding sites, locations, charge numbers, dynamic properties, the number of mutation needed, solvent accessibility, and side chain clashes.
  • one to two oxygen atoms from the solvent water molecules in the coordination shell may provide additional coordination without reducing the required binding affinity and selectivity.
  • Stronger metal ion binding affinities of the designed sites may be developed based on several modeled factors that contribute to metal ion affinity.
  • the number of ligand residues is a factor to directly chelate a specific metal ion.
  • the number of ligand residues is a factor to directly chelate a specific metal ion.
  • the number of charged residues is able to change metal ion affinity.
  • the ligand type is a factor as the binding preferences of a chelate may depend on the particular ligand type.
  • An illustrative version of this computational approach is the computerized (or otherwise automated) querying of one or more databases that comprise structural data on metal ion binding sites using selected criteria relevant to the metal ion binding site, generating at least one preliminary metal ion binding site from the database information based on compatibility with the selected criteria, and selecting one or more suitable metal ion binding sites from the preliminary metal ion binding sites based on optimal compatibility with the selected criteria.
  • the nucleic acid sequence of the selected metal ion binding site is obtained, tailored, and operatively linked with a scaffold protein sequence, whereby the nucleic acid sequence of the selected metal ion binding site is tailored so to achieve the metal ion binding site having a desired specificity for the metal ion.
  • a nucleic acid sequence encoding the preliminary binding sites can be generated from the structural or model data. The computational approach also can be used to produce the metal ion binding site.
  • the computational approach can be performed on or by a system comprising at least one database that comprises the structural data on metal ion binding sites, an algorithm for generating the preliminary metal ion binding sites from portions of the structural or model data using selected criteria relevant to the metal ion binding site and rating the preliminary metal ion binding sites based on specificity for a selected metal ion, and a computer for executing the algorithm so as to query the databases to generate the preliminary metal ion binding sites.
  • the algorithm generally is a relatively simple searching algorithm that will query the databases based on inputted criteria.
  • the grafting method focuses on engineering and constructing a metal ion binding site by modifying the primary, secondary, tertiary, and/or quaternary structure of an identified binding site. By selectively manipulating the structure of the binding site, it is possible to obtain a metal ion binding site that can be engineered into a scaffold protein, e.g., CD2 or fluorescent protein, without significantly denaturing the protein. Using the grafting method, it is possible to achieve a binding site that has a stronger preference for one metal ion over another metal ion. Such modifications may allow for improved contrast abilities.
  • a scaffold protein e.g., CD2 or fluorescent protein
  • an identified binding site for use with the grafting method may be any continuous sequence site that has some affinity for a metal ion.
  • binding sites may derive from either known binding peptides such as an individual EF-hand site or from short fragments that have demonstrated the ability to bind specific metal ions such as alpha-lactalbumin.
  • Such peptides may be highly conserved in nature and prevalent throughout nature or may be unnatural but known to have an affinity for a particular metal ion.
  • One of ordinary skill in the art is able to identify binding sites with affinity for a metal ion without undue experimentation.
  • the primary structure of the metal ion binding site may be altered and tuned to achieve a metal ion binding site with improved binding characteristics.
  • more charged ligand residues such aspartate and glutamate may be engineered by inserting codon(s) into the metal ion binding site so as to tune the responsiveness of the site or the scaffold protein.
  • the inclusion of additional charged ligands can allow the contrast agent to achieve an affinity for selected paramagnetic metal ions and to have a desired selectivity.
  • one or two water molecules can also be introduced into the coordination shell by removing or modifying ligand residues and their environments.
  • Further other mutations to the primary structure include removing or adding amino acids to change properties such as flexibility or rigidity of the site. Adding or removing amino acids from the binding site alters the primary structure of the binding site.
  • the secondary structure of the metal ion binding site may be modified to tune the sensitivity and responsiveness of the metal ion binding site.
  • the residues on the site itself, the flanking or the neighboring structures such as helices, beta strands, or turns may be modified by changing properties such as hydrophobicity, salt bridges, secondary structure propensity (e.g., helicity and ⁇ -sheets), and charge interactions with different amino acids, which all may inherently change the secondary structure.
  • the tertiary structure of the metal ion binding site may be modified to further tune the sensitivity and responsiveness of the metal ion binding site.
  • the affinity of the metal ion binding site for the metal ion may be varied by selectively manipulating and adding helices, loops, bridges and/or linkers and chemical properties such as hydrogen bonding, electrostatic interactions and hydrophobic interactions.
  • variations in tertiary structure may add stability and affinity by increasing secondary structure propensity, adding charge interaction of the side chains, and by stabilizing the metal ion binding coordination chemistry.
  • the dynamic properties can be modified by increasing the packing of the protein and replacing residues with amino acids or other moieties with more rigid (e.g., Pro) or flexible (e.g., Gly) properties,
  • One method of directly altering the primary, secondary, and/or tertiary structure of the metal ion binding site is by altering the charges in the site.
  • the charges in any binding site have a significant role in the structure of the site, changing the charges or charge ratio may have significant impact on the structure of the site.
  • the charged side chains exhibit a strong influence on the metal ion binding affinity even though they are not directly involved as ligands, the variation of these chains results in variations in metal ion binding affinities and selectivity.
  • a metal ion binding site may have stronger affinities to and better selectivity for a desired metal ion over a competitive metal ion by designing or modifying the site, e.g., changing the number of charged ligand residues to form metal ion binding pockets.
  • the metal ion binding affinity of the metal ion binding site may be varied by changing the charged side chains that are present on the metal ion binding site and/or the neighboring environment. The replacement of charged residues such as aspartate or glutamate with a residue such as alanine may dramatically reduce the binding affinity for the metal ion by up to 100 times.
  • the contrast agent in the case of multifunctional contrast agents, e.g., where the contrast agent is a fluorescent protein, it can be a factor to induce the metal binding site without altering significantly the chromophore environment to reduce the fluorescent signal.
  • These metal binding sites can be added at remote locations away from the chromophore or simply fusion to the fluorescent moieties. Such locations can be evident from the sequence and protein folding.
  • the grafting approach may be used with the design approach to create an optimal metal binding site.
  • metal binding sites can be created by using part of continuous site and part of ligand residues created by computer design.
  • the loops or any sequences of the proteins can be removed or modified to achieve optimal required binding affinity, metal selectivity, relaxivity and stability.
  • Natural metal binding proteins' their metal binding affinity can be altered by directly modifying the proteins such as the addition of metal ligand residues in the calcium binding proteins to increase metal binding affinity to lanthanides.
  • fragments and/or domains of the natural metal binding proteins encompassing metal binding sites can also serve as scaffold protein of the contrast agents if they exhibit strong metal binding affinity for Ln 3+ or other paramagnetic metal ions, serum stability, and desired relaxation properties.
  • the affinity to natural metal ions such as physiological metal ions, e.g., calcium, zinc, and magnesium, will be significantly reduced by deleting metal binding ligand residues or reducing the cooperativity between coupled metal binding sites.
  • the calcium binding sites in the natural calcium binding protein such as calmodulin and parvalbumin were modified so that the modified proteins have a strong metal binding affinity to lanthanides.
  • the metal selectivity for lanthanides over calcium, magnesium and zinc are very high. If it is necessary, the molecular recognition sites of these natural calcium binding proteins can be altered by deletion at the active sites or PEGylation.
  • sequences for N- and C-terminal domains of calmodulin and its variants are listed that can be serve as a protein contrast agents (See sequences included herein). Additional modifications can performed to reduce their intrinsic biological function, avoid immunogenicity, increase serum stability, and targeting capability.
  • the metal ion binding sites may be selectively introduced into numerous sites of a scaffold protein without substantially impairing its secondary structure.
  • a number of methods for identifying integration sites in proteins such CD2 proteins, fluorescent proteins (e.g., GFP, YFP, CFP, and RFP) are known in the art, including, for example, site directed mutagenesis, insertional mutagenesis, and deletional mutagenesis.
  • Other methods including the one exemplified below and in the Examples, are known or easily ascertained by one skilled in art.
  • the sites of the fluorescent protein that can tolerate the insertion of a metal ion binding site also may be determined and identified by gene manipulation and screening. By generating mutant proteins and by manipulating the DNA sequence, it is possible to obtain a variety of different insertions, which then may be screened to determine whether the protein maintains its intrinsic activities. Preferably, sites that remove or interfere with the intrinsic fluorescence of the fluorescent protein are not optimal and may be screened out. Variants identified in this fashion reveal sites that can tolerate insertions while retaining fluorescence.
  • the metal ion binding sites for use with scaffold proteins may be selected by considering five criteria so to as optimize the local properties of the metal binding site, the fluorescent protein, and the protein environment.
  • Third, the water coordination shell of the metal ion chelating sites should be able to coordinate at least 1-2 water molecules.
  • the residues from the loops between the secondary structures with good solvent accessibility are desired for both the folding of the protein and the fast kinetics required for the contrast agent.
  • the mutation or the introduction of the metal ion binding site should not substantially interfere with the synthesis and folding of the protein. More particularly, the introduction of the metal ion binding site does not interfere with either post-translational chromophore formation or intermolecular interactions required for stabilizing the chromophores and folding of the protein frame. Furthermore, the introduced side chain should not be overpacked and should not clash with the protein frame of the scaffold protein (e.g., the fluorescent protein).
  • the direct use of chromophore residues as chelating sites is not preferred but is within the scope of this disclosure.
  • the metal binding sites in the natural metal binding proteins can be directly modified to have proper metal binding affinity to the desired metal ions.
  • One or more metal ions are atoms and ions, including the respective isotopes and radioisotopes, that can bind to proteins or peptides.
  • a metal ion may bind reversibly or irreversibly and such a bond may be covalent or non-covalent.
  • Gd 3+ is used in some embodiments of this disclosure as an exemplary metal ion, it is understood that metal ions suitable with this disclosure include, but are not limited to metal ions including Group IIA metal ions, transition metal ions, and Lanthanide Series ions.
  • Exemplary metal ions include, but are not limited to, the ion, isotope, and/or radioisotope forms of magnesium, calcium, scandium, titanium, manganese, iron, boron, chromium, cobalt, nickel, cooper, zinc, gallium, strontium, yttrium, strontium, technetium, ruthenium, indium, hafnium, tungsten, rhenium, osmium, and bismuth.
  • radioisotopes include, but are not limited to, 64 Cu, 67 Cu, 67 Ga, 68 Ga, 88 Y, 89 Sr, 90 Y, 97 Ru, 99m Tc, 103 Ru, 111 In, 153 Sm, 186 Re, 188 Re, 203 Pb, 211 Bi, 212 Bi, 213 Bi, and 214 Bi.
  • the metal ions chosen to be chelated by the contrast agents depend in part on the diagnostic role of the metal ion.
  • Metals that can be incorporated, e.g., through chelation include lanthanides and other metal ions, including isotopes and radioisotopes thereof.
  • the preferred metal ion is gadolinium (III).
  • One of ordinary skill in the art can select a metal ion for chelation, based on the intended diagnostic application, without undue experimentation.
  • the choice of metal ions to be held in chelate complexes by the contrast agents of the disclosure depends upon the diagnostic technique for which the agent is to be used.
  • the metal ions should be paramagnetic, and preferably non-radioactive.
  • heavy metal ions e.g., with atomic numbers of at least 37, and in an embodiment, at least 50, should be used, again preferably non-radioactive species.
  • the metal ions should be ions of radioactive isotopes.
  • chelating groups For MR, X-ray, EIT or magnetometric imaging, one may use chelating groups to bind to heavy metal clusters (e.g., polyoxoanions and full or partial sulfur analogues) or to iron oxides or other superparamagnetic polyatomic species.
  • heavy metal clusters e.g., polyoxoanions and full or partial sulfur analogues
  • iron oxides or other superparamagnetic polyatomic species e.g., iron oxides or other superparamagnetic polyatomic species.
  • Metal may be incorporated into the contrast agent, i.e., the tailored binding sites, by direct incorporation, template synthesis, and transmetallation.
  • the metal ion is chelated into the contrast by direct incorporation, which involves titration with solution of sub-stoichiometric levels up to full incorporation.
  • one or two or more metal ions can bind to the contrast agent.
  • the contrast agent includes one or two or more metal ion binding sites.
  • each of the metal ion binding sites binds to the same metal ion.
  • each of the metal ion binding sites binds to a different metal.
  • Embodiments of the contrast agents can be used in any one of a number of methods.
  • Embodiments of this disclosure include, but are not limited to: methods of detecting, studying, monitoring, evaluating, and/or screening, diseases, conditions, and other biological events in vivo or in vitro.
  • the conditions can include, but are not limited to, altered growth rate of tissues, cancerous transformation of tissues, inflammation or infection of a tissue, altered volume of a tissue, altered density of a tissue, altered blood flow in a tissue, altered physiological function, altered metabolism of a tissue, loss of tissue viability, presence of edema or fibrosis in a tissue, altered perfusion in tissue, and combinations thereof.
  • embodiments of the present disclosure include: methods of imaging tissue; methods of diagnosing the presence of a disease, precancerous cells or tissue, cancer cells or tissue cancer, and tumors, as well as related biological events; methods of monitoring the progress of a disease, precancerous cells or tissue, cancer cells or tissue cancer, and tumors, as well as related biological events; and the like.
  • Embodiments of the present disclosure include, but are not limited to, imaging, detecting, studying, monitoring, evaluating, and/or screening biological materials (e.g., organs, tissues, tumors, cells, and the like), in vivo or in vitro.
  • biological materials e.g., organs, tissues, tumors, cells, and the like
  • the tissue types that can be studied using the methods of the present disclosure include, but are not limited to, myocardial tissues, nervous tissue, lymphoid tissue, skeletal and smooth muscle tissue, bones and cartilages, tissues of various organs (e.g., the kidney, the liver, the spleen, the prostate, the uterus, the testicles, and the ovaries), and select portions of each.
  • Embodiments of the methods can use one or more types of detecting or imaging systems such as, but not limited to, magnetic resonance imaging (MRI), SPECT, PET, ultrasound, X-ray, CAT, optical imaging, and combinations thereof.
  • the contrast agent is a multimodality contrast agent that includes a polymer having optical properties (GFP).
  • GFP polymer having optical properties
  • the polymer having optical properties can be detected using optical imaging, while the metal can be detected using another technique such as a MRI system.
  • embodiments of the contrast agent are administered to a host using one or more techniques or routes (e.g., oral, mucosal, parenteral, and the like).
  • the host can be introduced to an appropriate detection or imaging system.
  • the detection or imaging system can detect the contrast agent.
  • the detection or imaging system can detect the location(s) of the contrast agents, the concentration of the contrast agent, and the like.
  • the information obtained from the detection or imaging system can be used to create or form an image of the host or a portion thereof. The image would include the position and/or concentration of the contrast agent in the host.
  • the contrast agents can be used to study, image, diagnose the presence of, and/or treat cancerous cells or tissue, precancerous cells or tissue, cancer, or tumors.
  • the presence and location of the cancerous cells or tissue, precancerous cells or tissue, cancer, or tumors can provide insight into the appropriate diagnosis and/or treatment.
  • contrast agents could include targeting agents specific for other diseases or conditions so that other diseases or conditions can be imaged, diagnosed, and/or treated using embodiments of the present disclosure.
  • other diseases and/or conditions can be studied, imaged, diagnosed, and/or treated in a manner consistent with the discussion below as it relates to cancerous cells, precancerous cells, cancer, and/or tumors.
  • the contrast agent can be used to study, image, diagnose the presence of, and/or treat cancerous cells or tissue, precancerous cells or tissue, cancer, or tumors.
  • studying, imaging, diagnosing, and/or treating cancerous cells or tissue, precancerous cells or tissue, cancer, or tumors in a host the contrast agent is administered to the host in an amount effective to result in uptake of the contrast agent into the cancerous cells or tissue, precancerous cells or tissue, cancer, or tumors.
  • the cancerous cells or tissue, precancerous cells or tissue, cancer, or tumors that takes up the contrast agent is detected using an appropriate imaging system.
  • Embodiments of the present disclosure can non-invasively image the cancerous cells or tissue, precancerous cells or tissue, cancer, or tumors throughout a host.
  • the contrast agent includes a targeting agent having an affinity for a specific cancer. Detecting the presence of the contrast agent, in particular, the presence of the contrast agent at the typical location of the specific cancer can be used in the diagnosis of the presence of the cancer (or vice versa). Imaging the host over a time period (e.g., days, weeks, months, or years) can provide information about the progression of the cancer or other disease or condition.
  • the contrast agent or compositions including the contrast agent may be administered to a subject in an amount effective to achieve the desired result at the appropriate dosages and for the desired periods of time.
  • An effective amount of the contrast agent or compositions may vary according to factors such as the age, body weight, general health, sex, and diet of the host; the time of administration; the route of administration; the rate of excretion of the specific compound employed; the duration of the treatment; the existence of other drugs used in combination or coincidental with the specific compositions employed; the ability of the composition to elicit a desired response in the subject; and like factors well known in the medical arts.
  • An effective amount is also one in which any toxic or detrimental effects (e.g., side effects) of the contrast agent or compositions are outweighed by the therapeutically or diagnostically beneficial effects.
  • the contrast agent or compositions of the disclosure may be administered at a concentration of, for example, about 1 to 3.0 ⁇ mole/kg or about 6-20 mM.
  • Unit dosage forms of the contrast agents of this disclosure may be suitable for oral, mucosal (e.g., nasal, sublingual, vaginal, buccal, or rectal), parenteral (e.g., intramuscular, subcutaneous, intravenous, intra-arterial, or bolus injection), topical, or transdermal administration to a patient.
  • mucosal e.g., nasal, sublingual, vaginal, buccal, or rectal
  • parenteral e.g., intramuscular, subcutaneous, intravenous, intra-arterial, or bolus injection
  • topical e.g., topical, or transdermal administration to a patient.
  • dosage forms include, but are not limited to: tablets; caplets; capsules, such as hard gelatin capsules and soft elastic gelatin capsules; cachets; troches; lozenges; dispersions; suppositories; ointments; cataplasms (poultices); pastes; powders; dressings; creams; plasters; solutions; patches; aerosols (e.g., nasal sprays or inhalers); gels; liquid dosage forms suitable for oral or mucosal administration to a patient, including suspensions (e.g., aqueous or non-aqueous liquid suspensions, oil-in-water emulsions, or water-in-oil liquid emulsions), solutions, and elixirs; liquid dosage forms suitable for parenteral administration to a patient; and sterile solids (e.g., crystalline or amorphous solids) that can be reconstituted to provide liquid dosage forms suitable for parenteral administration to a patient.
  • suspensions e.g.,
  • composition, shape, and type of dosage forms of the contrast agents of the disclosure typically vary depending on their use.
  • a parenteral dosage form may contain smaller amounts of the active ingredient than an oral dosage form used to treat the same condition or disorder.
  • compositions including the contrast agent and dosage forms of the compositions of the disclosure can include one or more excipients.
  • Suitable excipients are well known to those skilled in the art of pharmacy or pharmaceutics, and non-limiting examples of suitable excipients are provided herein. Whether a particular excipient is suitable for incorporation into a composition or dosage form depends on a variety of factors well known in the art including, but not limited to, the way in which the dosage form will be administered to a patient.
  • oral dosage forms such as tablets or capsules, may contain excipients not suited for use in parenteral dosage forms.
  • the suitability of a particular excipient may also depend on the specific active ingredients in the dosage form. For example, the decomposition of some active ingredients can be accelerated by some excipients, such as lactose, or by exposure to water. Active ingredients that include primary or secondary amines are particularly susceptible to such accelerated decomposition.
  • compositions including the contrast agent and dosage forms of the compositions of the disclosure that can include one or more compounds that reduce the rate by which an active ingredient will decompose.
  • Such compounds which are referred to herein as “stabilizers,” include, but are not limited to, antioxidants such as ascorbic acid, pH buffers, or salt buffers.
  • pharmaceutical compositions or dosage forms of the disclosure may contain one or more solubility modulators, such as sodium chloride, sodium sulfate, sodium or potassium phosphate, or organic acids.
  • An exemplary solubility modulator is tartaric acid.
  • the amounts and specific type of active ingredient in a dosage form may differ depending on various factors. It will be understood, however, that the total daily usage of the compositions of the present disclosure will be decided by the attending physician or other attending professional within the scope of sound medical judgment.
  • the specific effective dose level for any particular host will depend upon a variety of factors, including for example, the activity of the specific composition employed; the specific composition employed; the age, body weight, general health, sex, and diet of the host; the time of administration; the route of administration; the rate of excretion of the specific compound employed; the duration of the treatment; the existence of other drugs used in combination or coincidental with the specific composition employed; and like factors well known in the medical arts. For example, it is well within the skill of the art to start doses of the composition at levels lower than those required to achieve the desired effect and to gradually increase the dosage until the desired effect is achieved.
  • kits which may include, but are not limited to, a contrast agent and directions (instructions for their use (written or electronic)).
  • the components listed above can be tailored to the particular disease or condition to be monitored.
  • the kit can further include appropriate reagents known in the art for administering various combinations of the components listed above to the host organism or patient.
  • This Example describes the rational design of a novel class of magnetic resonance imaging contrast agents with an engineered protein chelated with gadolinium.
  • the design of protein based contrast agents involves creating high coordination Gd 3+ binding sites in a stable host protein using amino acid residues and water molecules as metal coordinating ligands. Designed proteins show strong selectivity for Gd 3+ over physiological metal ions such as Ca 2+ , Zn 2+ , and Mg 2+ . These agents exhibit a 20-fold increase in longitudinal and transverse relaxivity values over the current clinically used contrast agent, Gd-DTPA. They provide strong contrast enhancement in vivo with much longer vascular retention time. These protein contrast agents have good biocompatibility and potential functionalities may extend MRI applications in targeting disease markers.
  • Magnetic resonance imaging is a non-invasive technique providing high resolution, three-dimensional images of morphological features as well as functional and physiological information about tissues in vivo. It is capable of detecting abnormalities in deep tissues and allows for whole body imaging. It has emerged as a primary diagnostic imaging technique for human diseases.
  • 1,2 Exogenous MRI contrast agents are often used to enhance the contrast between pathological and normal tissues by altering the longitudinal and transverse (i.e., T 1 and T 2 ) relaxation times of water protons.
  • 3-5 Gadolinium (Gd 3+ ) is the most frequently used MRI contrast agent due to its high magnetic moment, asymmetric electronic ground state and potential for increased MRI intensity.
  • the relaxivity (unit capability of the agent to change the relaxation time) of a contrast agent is dependent on several factors including the number of water molecules in the coordination shell, the exchange rate of the coordinated water with the bulk water, and the rotational correlation time ⁇ R of the contrast agent. 8-10 .
  • the MRI contrast agent can have: 1) high relaxivity for high contrast-to-noise ratio (CNR) and dose efficiency, 2) thermodynamic stability, especially metal selectivity for the target ions over excess physiological metal ions, to minimize the release of toxic paramagnetic metal ions, 3) adequate vascular, tissue retention time to allow imaging, and 4) proper excretion from the body.
  • Gd-DTPA the most commonly used MRI contrast agent in diagnostic imaging
  • Gd-DTPA-BMA the most commonly used MRI contrast agent in diagnostic imaging
  • ⁇ R the intrinsic rotational correlation time
  • these small molecular gadolinium contrast agents have longitudinal and transverse proton relaxivities, r 1 and r 2 , less than 10 mM ⁇ 1 s ⁇ 1 , much lower than the theoretically maximal value (>100 mM ⁇ 1 s ⁇ 1 ).
  • these small molecule contrast agents exhibit very short blood circulation (within several minutes) and tissue retention time, limiting some MRI applications that require longer data collection time.
  • This Example describes the development of a new class of MRI contrast agents with significantly improved relaxivity using rational design of Gd 3+ -binding proteins.
  • This class of contrast agents was created by designing the metal binding sites into a stable host protein with desired dynamic properties and metal selectivity to increase relaxivity by optimizing local ⁇ R . This approach provides a new platform for developing MRI contrast agents with high relaxivity and functionality.
  • Relaxation times, T 1 and T 2 were determined at 1.5, 3, 9.4 Tesla using a Siemens whole-body MR system (1.5, 3T) or a Bruker MRI scanner (9.4T). T 1 was determined using inversion recovery and T 2 using a multi-echo Carr-Purcell-Meiboom-Gill (CPMG) sequence.
  • the contrast agent samples (200 ⁇ l) with different concentrations were placed in eppendorf tubes. The tubes were placed on a tube rack, which was placed in MRI scanners for the measurement of relaxation times.
  • the number of water ligands coordinated to Gd 3+ -CA1.CD2 complex was determined by measuring Tb 3+ luminescence decay in H 2 O or D 2 O.
  • Tb 3+ excited state lifetime was measured using a fluorescence spectrophotometer (Photon Technology International, Inc.) with a 10 mm path length quartz cell at 22° C. Following excitation at 265 nm with a XenoFlash (Photon Technology International, Inc.), Tb 3+ emission was monitored at 545 nm in a time series experiment in both H 2 O and D 2 O systems.
  • Luminescence decay lifetime was obtained by fitting the acquired data with a mono-exponential decay function.
  • Gd 3+ -binding affinity of CA1.CD2 was determined by a competition titration with Fluo-5N applied as a Gd 3+ indicator.
  • the fluorescence spectra of Fluo-5N were obtained with a fluorescence spectrophotometer (Photon Technology International, Inc.) with a 10 mm path length quartz cell at 22° C. Fluo-5N emission spectra were acquired at 500 nm to 650 nm with an excitation at 488 nm.
  • Gd 3+ -binding affinity of Fluo-5N, K d1 was first determined by a Gd 3+ titration with Gd 3+ buffer system of 1 mM nitrilotriacetic acid (NTA). Free Gd 3+ concentration was calculated with a NTA Gd 3+ -binding affinity of 2.6 ⁇ 10 ⁇ 12 M. 28 Fluo-5N was mixed with Gd 3+ in 1:1 ratio for a competition titration. The experiment was performed with a gradual addition of CA1.CD2. An apparent constant, K app , was estimated by fitting the fluorescence emission intensity of Fluo-5N at 520 nm with different CA1.CD2 concentrations as a 1 to 1 binding model. Gd 3+ -binding affinity of CA1.CD2, K d2 , was calculated with the following equation:
  • K d ⁇ ⁇ 2 K app ⁇ K d ⁇ ⁇ 1 K d ⁇ ⁇ 1 + [ Fluo - 5 ⁇ N ] T ( 1 )
  • mice 25-30 g, four mice were imaged
  • the anesthetized animal was positioned and stabilized with soft-supporting material (e.g., foam) in the scanner in the coil cradle and was kept warm during the MRI scan.
  • the mice were scanned prior to the administration of any contrast agent (pre-contrast).
  • any contrast agent pre-contrast.
  • Gd-CA1.CD2 ⁇ 1.2 mM
  • Gd-DTPA ⁇ 300 mM
  • T 2 weighted imaging at 9.4T MR images were recorded using a multi-echo Carr-Purcell-Meiboom-Gill (CPMG) sequence. The data were collected and processed by Dicomworks software. The MR signal intensity in several organs was ascertained by the average intensity in ROIs or points within the organs. Signal intensity for each organ was normalized to that of the leg muscle.
  • CPMG Carr-Purcell-Meiboom-Gill
  • the organ/tissue samples were collected. Tissue extracts were freshly made from collected samples using commercially available tissue extracting kits (Qiagen).
  • CA1.CD2 was detected and quantified by immunoblotting and Sandwich-ELISA using a monoclonal antibody (OX45, detecting antibody) and a home made polyclonal antibody (PabCD2, capture antibody).
  • OX45 monoclonal antibody
  • PabCD2, capture antibody a home made polyclonal antibody
  • a series of known amounts of CA1.CD2 samples mixed with blank mouse serum or tissue extracts were used as standard in Sandwich-ELISA.
  • ELISA signal from HRP was monitored using a Fluorstar fluorescence microplate reader.
  • mice that received the i.v. administered Gd-CA1.CD2 (at a dose of ⁇ 2.4 ⁇ mol/kg) were returned to their cages (one mouse per cage). The mice were observed for five days and were euthanized at the end of the fifth day. Tissue samples from kidney, liver, spleen, and lung were collected. Gd 3+ ion contents in the tissue samples were analyzed by ICP-MS (see above paragraph).
  • mice Two groups of mice were used to examine potential renal and/or liver damage by Gd-CA1.CD2.
  • ALT Alanine transaminase
  • ALP Alkaline phosphatase
  • AST Aspartate transaminase
  • GTT Gamma glutamyl transpeptidase
  • bilirubin and urea nitrogen were analyzed by a commercially available source (MU Research Animal Diagnostic Laboratory). All clinical chemistry parameters were measured on an Olympus AU 400 analyzer.
  • Cytotoxicity was analyzed by MTT assay of the cells that were treated with Gd-CA1.CD2 at appropriate doses (indicated in figure).
  • the cells were grown under normal growth medium in 96 well plates.
  • Gd-CA1.CD2 or saline-phosphate buffer was added to the cell culture medium. The cells were incubated for appropriate times.
  • a standard MTT assay was employed to assess the cell growth status of the treated cells.
  • CA1.CD2 (40 ⁇ M) in complex with Gd 3+ was incubated with 75% human serum over 3 or 6 hours at 37° C.
  • the degradation of the protein was analyzed by SDS-PAGE and visualized by coomassie blue staining.
  • the degradation of the protein was also analyzed by immunoblot using antibodies OX54 or PabCD2.
  • the identities of the 12 kDa bands as CA1.CD2 were always verified by immunobloting using antibody PabCD2.
  • FIG. 1.1 shows the simulation of the dependence of r 1 and r 2 on the rotational correlation time, ⁇ R , of a contrast agent at different magnetic field strengths according to the theory developed by Blombergen, Solomon 6,7 (for detailed simulation procedures, please see on-line supporting materials).
  • ⁇ R the rotational correlation time
  • the relaxivity is ⁇ 10 mM ⁇ 1 s ⁇ 1 regardless of how the other parameters are adjusted.
  • the simulation clearly suggests that contrast agents with ⁇ R of 10-50 ns have the highest r 1 and r 2 values at clinically relevant magnetic field strengths from 0.47-4.7 Tesla (T).
  • high-relaxivity MRI contrast agents can be developed by directly designing Gd 3+ binding sites in proteins with desired ⁇ R . Coordinating Gd 3+ ions directly to the rigid protein frame eliminates the high internal mobility associated with chelator-macromolecule conjugates ( FIG. 1.1 a ).
  • CD2 rat CD2
  • a cell adhesion protein with a common immunoglobin fold as a scaffold
  • FIG. 1.1 c a cell adhesion protein with a common immunoglobin fold
  • CD2 protein exhibits strong stability against pH changes and excellent tolerance against various mutations, 29 which are essential features of functional protein engineering.
  • ⁇ R rotational correlation time
  • ⁇ R rotational correlation time
  • ⁇ 10 ns corresponding to optimal relaxivity for the current clinically allowed magnetic field strength.
  • its molecular size (12 kDa) is suitable for good tissue penetration and easy renal exclusion. 17
  • Gd 3+ binding sites into CD2 using computational methods.
  • 32,33 The design was based on the established structural parameters obtained from detailed analysis of metal binding sites in over 500 small chelators and metalloproteins.
  • Gd 3+ , Tb 3+ , La 3+ and other Ln 3+ ions have coordination properties similar to those of Ca 2+ with a strong preference for oxygen ligand atoms.
  • DTPA has 5 oxygen ligand atoms and 2 nitrogen ligand atoms.
  • the coordination atoms are almost always oxygen atoms, and the coordination numbers are lower than small chelators with an average of 7.2 for Ln 3+ and 6.0-6.5 for Ca 2+ . These effects are possibly due to steric crowding and sidechain packing. 34 Previously, we successfully designed Ca 2+ and Ln 3+ binding sites in a scaffold protein with strong selectivity over excess physiological metal ions. 35 Structure determination by solution NMR revealed that the actual coordination geometry in a designed variant is the same as our design, verifying the computational methods and the design strategy of metal-binding sites in proteins. 31
  • FIG. 1.1 c shows an example of designed Gd 3+ -binding protein CA1.CD2 with a metal binding site formed by the six potential oxygen ligands from the carboxyl side chains of Glu15, Glu56, Asp58, Asp62 and Asp64.
  • 36 we placed 5 negatively charged residues to provide these six oxygen ligand atoms in the coordination shell of CA1.CD2 to increase the selectivity for Gd 3+ over Ca 2+ .
  • one position of the metal binding geometry was left open in the design to allow fast water exchange between the paramagnetic metal ion and the bulk solvent ( FIG.
  • the Gd 3+ -binding site has minimal internal flexibility as the ligand residues originate from rigid stretches of the protein frame.
  • another Gd 3+ -binding protein, CA9.CD2 was engineered by fusing a continuous cation-binding EF-hand loop from calmodulin with flexible glycine linkers to the host protein. 37,38 This protein mimics previously reported highly flexible chelate-based contrast agents conjugated to macromolecules. 24,25
  • CA1.CD2 exhibited disassociation constants (K d ) of 7.0 ⁇ 10 ⁇ 13 , 1.9 ⁇ 10 ⁇ 7 , 6 ⁇ 10 ⁇ 3 , and >1 ⁇ 10 ⁇ 2 M for Gd 3+ , Zn 2+ , Ca 2+ , and Mg 2+ , respectively.
  • the selectivity K d ML /K d GdL for Gd 3+ over physiological divalent cations Zn 2+ , Ca 2+ , and Mg 2+ are 10 5.34 , >10 9.84 , and >10 10.06 , respectively.
  • the metal selectivity of CA1.CD2 is significantly greater than or comparable to that of FDA approved contrast agents DTPA- and DTPA-BMA 40 (Table 1).
  • Example 1 Metal binding constants (Log K a ) and metal selectivity of DTPA, DTPA-BMA and CA1.
  • CD2 Log Log Log Log Sample Gd 3+ Zn 2+ Ca 2+ Mg 2+ (K Gd /K Zn ) (K Gd /K Ca ) (K Gd /K Mg ) DTPA 28 22.45 18.29 10.75 18.20 4.17 11.70 4.25 DTPA-BMA 41 16.85 12.04 7.17 na* 4.81 9.68 na* CA1.CD2 12.06 6.72 ⁇ 2.22 ⁇ 2.0 5.34 >9.84 >10.06 *na: not available.
  • the designed Gd-binding proteins exhibit high r1 and r2 relaxivity.
  • FIG. 1.2 a shows that, at a concentration of 50 ⁇ M, the designed contrast agents Gd-CA1.CD2 and Gd-CA2.CD2 were able to introduce contrast enhancement in T1 weighted imaging at 3.0 T while 100 ⁇ M Gd-DTPA and protein CA1.CD2 alone did not lead to significant enhancement.
  • the in vitro relaxivity values of the designed Gd-binding proteins were measured (Table 2).
  • Gd-CA1.CD2 exhibits r 1 up to 117 mM ⁇ 1 s ⁇ 1 at 1.5T, about 20-fold higher than that of Gd-DTPA.
  • Gd-CA9.CD2 which carries a flexibly-conjugated Gd 3+ -binding site, had significantly lower relaxivity values (3.4 and 3.6 mM ⁇ 1 s ⁇ 1 , for r1 and r2 respectively, at 3.0 T), that are comparable to those of Gd-DTPA (Table 2).
  • the r 1 and r 2 of Gd-CA1.CD2 exhibited an inverse relationship with the magnetic field strength (Table 2, Example 1).
  • the r 1 and r 2 of Gd-DPTA showed weak dependence on field strengths.
  • the magnetic field strength dependent changes in relaxivity are consistent with our simulation results based on the rotational ⁇ R of the contrast agent ( FIG. 1.1 b ).
  • the results showed that the protein contrast agent offers much higher relaxivities for MRI contrast enhancement at clinical magnetic field strengths (1.5-3.0 T).
  • the transverse relaxivity of designed contrast agent is very high (i.g. >50 mM ⁇ 1 s ⁇ 1 ) at 9.4T compared to Gd-DTPA, making it appropriate as a T 2 contrast agent (Table 2) at high fields.
  • r2 of our protein-based contrast agent is smaller than the currently used r2 agents such as iron oxides. 42 This property allows our contrast agents to fill a gap between small Gd-chelators and iron oxide nanoparticles, extending the range of MRI applications both at clinically relevant field strength and possibly higher field strength.
  • the hydration number of an MRI contrast agent is another determinant for r 1 and r 2 .
  • the hydration number of the designed protein-based contrast agents was determined by measuring the luminescence lifetime of Tb 3+ . 26
  • the free Tb 3+ in H 2 O and D 2 O has a life time value of 410 ⁇ s and 2,796 ⁇ s, respectively.
  • the formation of M-protein complex significantly increases Tb 3+ life time to 859 ⁇ s.
  • the Tb 3+ life time values of CA1.CD2 were 1,679 ⁇ s in D 2 O, suggesting a hydration number of 2.1 ( FIG. 1.3 b ).
  • a well-known Ca 2+ -binding protein troponin C exhibits a hydration number of 1.8 ( FIG.
  • Gd-CA1.CD2 was sustained over 4-7 hours at multiple organs ( FIG. 1.8 b ), indicating much longer tissue retention time of the agent than that of Gd-DTPA.
  • the tissue retention and blood circulation time of Gd-CA1.CD2 in mice were characterized by administering various doses of agents in mice and analyzing the collected blood samples or tissue sections from sacrificed animals using immunoblots and ELISA with monoclonal (OX45) and in-house developed polyclonal (PabCD2) antibodies.
  • OX45 monoclonal
  • PabCD2 polyclonal
  • Gd-CA1.CD2 exhibited a prolonged blood circulation time. No significant decrease in the CA1.CD2 levels in blood was observed until 45 minutes after i.v. administration.
  • the protein remained in blood circulation for more than 3 hours ( FIG. 1.8 a ). This property is considered for imaging of biological events that require prolonged imaging time, or imaging of pathological features that require time for delivery of the agent to the targeted site.
  • CA1.CD2 was first detectable at 15 minutes and peaked at 4-5 hours. There was less than 10% of the injected dose of the contrast agent remaining in the kidney 15 hours after injection (by measurements of both Gd 3+ and CA1.CD2). This result, along with the observation of MRI contrast changes in the bladder, suggests a clearance of the agent by kidney.
  • Gd-CA1.CD2 did not exhibit acute toxicity at the dose ( ⁇ 2.4 ⁇ mole/kg) used for MRI. All mice that received the contrast agents (>10) showed no adverse effects before euthanization five days after agent injection. The effects of Gd-CA1.CD2 on liver enzymes (ALT, ALP, AST), serum urea nitrogen, bilirubin, and total protein from CD-1 mice 48 hours post-contrast injection were negligible compared to those in the control mice (Example 1, Table 3). In addition, no cytotoxicity was observed in tested cell lines, SW620, SW480 and HEK293, that were treated with 50 ⁇ M Gd-CA1.CD2, by MTT assay ( FIG. 1.8 b ). Based on the preliminary characterization of toxicity, we conclude that the protein contrast agent did not possess acute toxicity at current dosages for mice.
  • Example 1 Summary of Animal Clinical Pathology Profiles Test mice a Control mice b Normal rang c Urea Nitrogen (mg/L) 26.0 ⁇ 0.2 d 27.0 ⁇ 0.2 18-31 Total Urine Protein 5.2 ⁇ 0.2 5.3 ⁇ 0.2 5.9-10.3 (g/L) Total Bili (mg/L) 0.4 ⁇ 0.2 0.5 ⁇ 0.2 0.3-0.8 Direct Bili (mg/L) 0.0 0.0 0.0 ALT (U/L) 49.0 ⁇ 0.2 72.0 ⁇ 0.2 44-87 ALP (U/L) 115.0 ⁇ 0.2 302.0 ⁇ 0.2 43-71 AST (U/L) 280.0 ⁇ 0.2 219.0 ⁇ 0.2 101-214 GGT (U/L) 0.0 ⁇ 3.0 a Four mice per group were injected with Gd-CA1.CD2 at dose of 4.0 ⁇ mole/kg.
  • mice All clinical chemistry parameters are measured on an Olympus AU 400 analyzer by MU Research Animal Diagnostic Laboratory (details see Material and Methods).
  • c Normal range values are from Quesenberry, K. E. and J. W. Carpenter; Ferrets, Rabbits, and Rodents Clinical Medicine and Surgery; W. B. Saunders: Philadelphia, 2003.
  • Using protein to chelate Gd 3+ as an MRI contrast agent has several potential advantages over currently used Gd-DTPA in functional and molecular imaging applications: 1) it greatly increases the contrast-to-noise ratio (CNR); 2) it improves dose efficiency with reduced metal toxicity; 3) it prolongs the tissue retention time, which enables imaging of abnormalities that requires prolonged tissue enhancement; and 4) provide a potential functioning protein or a protein carrier that can conjugate target specific ligands to a biomarker for targeted molecular MR imaging.
  • CNR contrast-to-noise ratio
  • R 1 cq 55.5 ⁇ 1 T 1 ⁇ m + ⁇ m ( 1 )
  • R 2 cq 55.5 ⁇ T 2 ⁇ m - 2 + ⁇ m - 1 ⁇ T 2 ⁇ m - 1 + ⁇ ⁇ ⁇ ⁇ m 2 ⁇ m ⁇ ( ( ⁇ m - 1 + T 2 ⁇ m - 1 ) 2 + ⁇ ⁇ ⁇ ⁇ m 2 ) ( 2 )
  • Equation 2 the water coordination number, q, is assumed to be 1 and the agent concentration is 0.001 M; ⁇ m is the dwelling time of the coordination water; and ⁇ m is the chemical shift difference between the bound and free water. Since ⁇ m 2 is much smaller than other components, equation 2 is simplified to supplementary equation 3 and used in this simulation:
  • T im is determined by dipole-dipole (DD) and scalar or contact (SC) mechanisms as shown in supplementary equation 4:
  • the frequency of proton ⁇ 1 equals to the ⁇ 1 multiplied by the magnetic field while the frequency of electron ⁇ s is 658-fold of ⁇ 1 .
  • the ⁇ ci is determined by the rotational correlation time ⁇ R , the water dwelling time ⁇ m , and T ie as shown in supplementary equation 7:
  • T ie is related to the electron frequency ⁇ s as well as the ⁇ v (correlation time of splitting) and ⁇ 2 (mean square zero field splitting energy) of the Gd 3+ as in supplementary equations 8-10:
  • ⁇ R (1 ps, 10 ps, 100 ps, 1 ns, 10 ns, and 100 ns
  • ⁇ m (1 ps, 10 ps, 100 ps, 1 ns, 10 ns, and 100 ns
  • ⁇ v (1 and 10 ps)
  • ⁇ 2 10 17 , 10 18 , 10 19 , and 10 20 s ⁇ 2
  • the relaxivity is ⁇ 10 mM ⁇ 1 s ⁇ 1 no matter how the other parameters are adjusted.
  • the relaxivity can reach a much higher level by adjusting other parameters such as the ⁇ m .
  • the protein contrast agent Gd-CA1.CD2 did not exhibit acute toxicity at the MRI imaging dose ( ⁇ 2.4 mole/kg), as demonstrated by the fact that all MR imaged mice that received the contrast agent (>10) behaved normally and remained healthy (sacrificed five days after agent injection).
  • the effects of Gd-CA1.CD2 on liver enzymes (ALT, ALP, AST), serum urea nitrogen, bilirubin, and total protein from CD-1 mice 48 hours post-contrast injection were negligible compared to the control mice (Table 3).
  • no cytotoxicity was observed in tested cell lines, SW620, SW480 and HEK293 that were treated with 50 ⁇ M Gd-CA1.CD2, by MTT assay ( FIG. 1.7 b ). Based on the preliminary characterization of toxicity, we conclude that the protein contrast agent is relatively safe.
  • PEGylation of protein is a method used to improve the pharmacokinetics and pharmaco-dynamics of various protein and peptide drugs.
  • PEGylation involves modifications of Lys, Glu, Asp, or Cys residues of a protein or peptide with various sizes of polyethylene glycerol chain.
  • the result of PEGylation modifications is the attachment of the different size of polyethylene glycerol chains on the surface of the modified protein or peptide.
  • the protein or peptide experiences several property changes, especially in pharmacokinetics and pharmaco-dynamics. Two changes are obvious: (1) the increase in molecular size, especially in the case of small peptide, and (2) the reduction in surface charges of protein and peptide.
  • Protein was expressed in E. coli as inclusion body and purified using urea refolding and ion-exchange column. N15 labeled protein was expressed in SV medium as GST fusion (Yang et al., Biochem 2006) and purification was by GST-4B affinity column and SP column. Protein was verifed by mass spectrometry. Protein concentration was calculated using extinction coefficient of w.t. CD2 of 11,000 (Ye et al., 2001). Protein solubility was determined by concentrating proteins to reach to precipitation using speed vac.
  • ESI and MALDI spectrometry were used to identify the number of pegylation sites and metal binding stoichiometry.
  • the pegylation sites were identified using trypsin cleavage followed by Mass analysis using TOF/TOF.
  • Gd 3+ -binding affinities of CA1.CD2 and its pegylated variants were determined by a competition titration with Fluo-5N applied as a Gd 3+ indicator (Yang et al., JACS, 2008).
  • the fluorescence spectra of Fluo-5N were obtained with a fluorescence spectrophotometer (Photon Technology International, Inc.) with a 10 mm path length quartz cell at 22° C. Fluo-5N emission spectra were acquired at 500 nm to 650 nm with an excitation at 488 nm.
  • Gd 3+ -binding affinity of Fluo-5N, K d1 was first determined by a Gd 3+ titration with Gd 3+ buffer system of 1 mM nitrilotriacetic acid (NTA). Free Gd 3+ concentration was calculated with a NTA Gd 3+ -binding affinity of 2.6 ⁇ 10 ⁇ 12 M. 28 Fluo-5N was mixed with Gd 3+ in 1:1 ratio for a competition titration. The experiment was performed with a gradual addition of CA1.CD2 or its variants. An apparent constant, K app , was estimated by fitting the fluorescence emission intensity of Fluo-5N at 520 nm with different CA1.CD2 concentrations as a 1 to 1 binding model. Gd 3+ -binding affinity of CA1.CD2, K d2 , was calculated with the following equation:
  • K d ⁇ ⁇ 2 K app ⁇ K d ⁇ ⁇ 1 K d ⁇ ⁇ 1 + [ Fluo - 5 ⁇ N ] T ( 1 )
  • the numbers of water ligands coordinated to Gd 3+ -CA1.CD2 and variants complex were determined by measuring Tb 3+ luminescence decay in H 2 O or D 2 O (Yang et al., 2008).
  • Tb 3+ excited state lifetime was measured using a fluorescence spectrophotometer (Photon Technology International, Inc.) with a 10 mm path length quartz cell at 22° C. Following excitation at 265 nm with a XenoFlash (Photon Technology International, Inc.), Tb 3+ emission was monitored at 545 nm in a time series experiment in both H 2 O and D 2 O systems.
  • Luminescence decay lifetime was obtained by fitting the acquired data with a mono-exponential decay function.
  • Pulse field diffusion NMR was applied to measure the hydrodynamic radii of the protein (Lee et al., BBA 2003) with Protein samples CA1.CD2 and its variants of 0.2 mM in buffer. Lysozme and diaxone were used as an external and internal reference for calibration. The correlation size of the protein was measured using TauC pulse sequence developed by the Prestegard lab at UGA using 15 N labeled protein.
  • CD-1 mice 25-30 g, four mice were imaged
  • the anesthetized animal was positioned and stabilized with soft-supporting material (e.g. foam) in the scanner in the coil cradle and was kept warm during the MRI scan.
  • the mice were scanned prior to the administration of any contrast agent (pre-contrast).
  • any contrast agent pre-contrast.
  • Gd-CA1.CD2 ⁇ 1.2 mM
  • Gd-DTPA ⁇ 300 mM
  • T 2 weighted imaging at 9.4T MR images were recorded using a multi-echo Carr-Purcell-Meiboom-Gill (CPMG) sequence. The data were collected and processed by Dicomworks software. The MR signal intensity in several organs was ascertained by the average intensity in ROIs or points within the organs. Signal intensity for each organ was normalized to that of the leg muscle.
  • CPMG Carr-Purcell-Meiboom-Gill
  • CD-1 mice 25-30 g were anesthetized with isoflurane. Appropriate dosages of Gd-CA1.CD2 and its PEgylated variants (with Gd and 153 Gd) or Gd-DTPA were i.v. injected (via tail vein). Blood ( ⁇ 50 ⁇ l) samples were collected via orbital sinus of the mouse at different time points. The mouse was euthanized at the final time point. Tissue samples from kidney, liver, heart, and lung were collected. Serum samples were prepared from the collected blood. For the bio-distribution analyses, the animals were euthanized at single time point (indicated) after i.v. administration of the contrast agent (indicated). The organ/tissue samples were collected.
  • Tissue extracts were freshly made from collected samples using commercially available tissue extracting kits (Qiagen).
  • CA1.CD2 and its variants were detected and quantified by immunoblotting and Sandwich-ELISA using a monoclonal antibody (OX45, detecting antibody) and a home made polyclonal antibody (PabCD2, capture antibody).
  • OX45 monoclonal antibody
  • PabCD2, capture antibody a home made polyclonal antibody
  • a series of known amounts of CA1.CD2 samples mixed with blank mouse serum or tissue extracts were used as standard in Sandwich-ELISA.
  • ELISA signal from HRP was monitored using a Fluorstar fluorescence microplate reader.
  • Rabbits were i.p. injected with Gd-CA1.CD2 and its pegylated variants.
  • the agents (CA1.CD2) were mixed with adjuvant or with buffer saline and injected at a dose of 3.0 nmole/kg according to the standard protocol for the antibody production.
  • the rabbits were subjected to double immunolizations in four weeks interval. Blood samples were taken from the immunolized rabbits 3 weeks after each injection. Production of antibodies against the protein contrast agent in each rabbit was examined by ELISA
  • the MR imaged CD-1 mice that received the i.v. administered Gd-CA1.CD2 and its variants (at a dose of ⁇ 2.4 ⁇ mol/kg) spiked with 157 Gd 3+ were returned to their cages (one mouse per cage). The mice were observed for five days and were euthanized at the end of the fifth day. Tissue samples from kidney, liver, spleen, and lung were collected. Gd 3+ contents in the tissue samples were analyzed by radioactivity counter.
  • mice Two groups of mice were used to examine potential renal and/or liver damage by Gd-CA1.CD2.
  • ALT Alanine transaminase
  • ALP Alkaline phosphatase
  • AST Aspartate transaminase
  • GTT Gamma glutamyl transpeptidase
  • bilirubin and urea nitrogen were analyzed by a commercially available source (MU Research Animal Diagnostic Laboratory). All clinical chemistry parameters were measured on an Olympus AU 400 analyzer.
  • Cytotoxicity was analyzed by MTT assay of the cells that were treated with Gd-CA1.CD2 and its variants at appropriate doses (indicated in figure).
  • the cells were grown under normal growth medium in 96 well plates.
  • Gd-CA1.CD2 or saline-phosphate buffer was added to the cell culture medium. The cells were incubated for appropriate times.
  • a standard MTT assay was employed to assess the cell growth status of the treated cells.
  • CA1.CD2 (40 ⁇ M) in complex with Gd 3+ was incubated with 75% human serum over 3 or 6 hours at 37° C.
  • the degradation of the protein (disappearance of 12 kDa protein band) was analyzed by SDS-PAGE and visualized by coomassie blue staining for protein and idiol staining for PEG moiety.
  • the degradation of the protein was also analyzed by immunoblot using antibodies OX54 or PabCD2.
  • the identities of CA1.CD2 and pegylated variants were verified by immunobloting using antibody PabCD2 and idiol staining.
  • the contrast agents exhibit a 20 fold increase in R1 and R2 relaxivities and provide a strong contrast enhancement in the mouse MR imaging (Yang, et. al. JACS 2008).
  • the developed MRI contrast agent also demonstrated a prolonged blood circulation time, which is considered for the application of the agents in disease targeted molecular imaging.
  • DTPA 300-500 mM
  • the solubility of the current formulation of our protein contrast CA1.CD2 is ⁇ 0.7 mM.
  • the designed contrast agent CA1.CD2 has eight Lys residues with different solvent accessibility and six Lys residues are well exposed. Based on the considerations of solubility, circulation, relaxivity and serum stability, we therefore carried out PEGylation of our protein contrast agents by modifying surface Lys residues and site specific pegylation. First, preactivated PEG units with varied chain length and branches of 4, 12 (Poly-PEG 12 ), 40 (PolyPEG 40k ), 5K, and 12 K (see FIG. 2.1 b ) were used to modify surface lys residues. Site-specific pegylation was performed at both N-terminal Lys and C-terminal Cys.
  • FIGS. 2 . 2 - 2 . 4 shows the SDS gel of the protein contrast agent CA1.CD2 pegylated with PEGylation kits with different reaction moieties stained by both commassie blue for protein and idiol for the PEG moiety.
  • FIG. 2.2 shows that the PEGylated proteins were separated using ion exchange column, size exchange column, and a C 18 reverse phase HPLC chromatography column. The modified proteins were purified by HPLC to relative homogeneity.
  • FIG. 2.2 shows that there were several major peaks of the PEGylated proteins on the FPLC chromatography. MALD-Mass analyses of the separated protein fraction reveal that at pH 7.4 with 5:1 pEG:protein:preactivated pEG reagents, CA1.CD2 was pegylated mainly with 2, 3 with P4-P40 and 1 PEG unit with PEG 12 K to 20K.
  • the CA1.CD2 has total of seven potential PEGylation sites.
  • the PEGylation sites of the purified protein were examined first by trypsin cleavage to generate the peptides/fragments and then sequenced by TOF/TOF MS. Usually 2-4 PEG units were attached to each protein depending on the ratio of PEG:protein under reaction and the reaction conditions.
  • FIG. 2.4 a of Trp fluorescence spectra shows that these PEGylated proteins (CA1.CD2-PEG12 and CA1.CD2-PEG40) maintain the native structure of the protein contrast agents with unchanged Trp emission maximum compared with CA1.CD2.
  • Tb-FRET was first used to monitor the effect of pegylation on the metal binding capabilities.
  • the pegylated A1.CD2 is able to have Tb-sensitized energy transfer similar to that of CA1.CD2.
  • FIG. 2.5 shows that PEGylated CA1.CD2-P40 remains intact after incubate with human serum for 24 hours at 37° C. monitored by SDS Page.
  • Gd 3+ -binding affinity of CA1.CD2 was further determined by a competition titration with fluorescent dye applied as a Gd 3+ indicator in various chelate-metal buffer systems.
  • the PEGylated variants exhibit similar metal binding affinities to unpegylated ones for Ca 2+ , Gd 3+ and Zn 2+ .
  • FIG. 2.6 shows the R1 and R2 relaxivities of the PEGylated protein.
  • the R1 and R2 relaxivities of the PEGylated protein were also affected by the size of the PEG chains.
  • the relaxivities of the PEGylated protein contrast agents demonstrated higher increases when the protein was modified by a longer PEG chain.
  • both R1 and R2 relaxivities of the PEGylated protein contrast agent experienced the most dramatic increases at higher magnetic field. This is contrary to the case of unPEGylated protein, in which dramatic decreases in R1 and R2 relaxivities were observed at high field (Yang et al., JACS, 2008).
  • FIG. 2.6 shows the MRI relaxivity as a function of chain dependencies. Specific modification of the N-terminal amine and Cys residues at the C-terminus have a similar effect on the relaxivity of the protein.
  • Table 2.1 of Example 2 shows that the water numbers in the coordination shell of CA1.CD2 increased from 2 to 3 upon PEGylation with PEG40. This may contribute to the increased relaxivity by PEGylation.
  • PEGylation has been demonstrated to increase blood circulation time and reduce immunogenicity of a number of protein drugs. While longer blood circulation time is a desired property for the applications of MRI contrast agents. Elimination or reduction of immunogenicity is essential for clinical applications of the protein MRI contrast agents.
  • PEGylation of CA1.CD2 changed the bio-distribution and immunogenicity properties of the agent.
  • the PEGylated or unPEGylated CA1.CD2 was introduced to CD-1 mice via i.v. tail vein injection.
  • Immunogenicity is one of the main concerns on the application of our developed protein MRI contrast agent.
  • the agents (CA1.CD2) were mixed with adjuvant or with buffer saline and injected at a dose of 3.0 nmole/kg according to the standard protocol for antibody production.
  • the rabbits were subjected to double immunolizations in four weeks interval. Blood samples were taken from the immunolized rabbits 3 weeks after each injection. Production of antibodies against the protein contrast agent in each rabbit was examined by ELISA ( FIG. 2.7 Left) and Immunobloting ( FIG. 2.7 Right) using our previous polyclonal antibody PabCD2 as positive control and the pre-bleed from each rabbit as negative controls.
  • FIG. 2.7 shows that PEGylation with P40 completely eliminates the binding of CA1.CD2 by antibody OX55 and decreases by 50% binding of OX34 in Western Blot. Since the epitope binding sites of OX55 and OX34 are well known, we have shown that K66, K45, K44, and K47 exhibit a high probability for the specific PEGylation by PEG12. These results confirm that antibody recognition sites can be eliminated by PEGylation, which is essential for the reduction of immunogenicity.
  • Natural calcium binding proteins with continuous calcium binding sites such as calmodulin, calbindin D9K, troponin C, parvalbumin and discontinuous calcium binding sites such as thermintase subtilisin have exhibited high metal binding affinity for calcium as shown in Table 3.1 (shown in FIG. 3.10 ). Most of these calcium binding proteins have multiple calcium binding sites and their protein stabilities against temperature and proteolysis were significantly increased. For example, calcium binding to calmodulin has increased its stability to higher than 100° C. While a great deal of research has shown that the calcium binding affinity of naturally evolved proteins can be reduced by site-directed mutagenesis, methods to increase calcium binding affinity have rarely been reported.
  • CBPP and its variants exhibit strong metal selectivity for Ln3+ over calcium, magnesium, zinc and copper ( FIG. 3.2 c ). Furthermore, the water numbers in the coordination site can be estimated by Tb-sensitized energy transfer in water and in D 2 O. These data suggest that more than one water molecules are in the coordination shells and protein surface, and this likely contributes to their extremely high relaxivity.
  • FIG. 3.8 shows that calmodulin and its variants can be pegylated with peg units of 4, 12, 40, 5K, 12K, 20 K and reaction products can be well separated by size-exclusion and ion exchange columns ( FIG. 3.3 and FIG. 3.4 ).
  • FIG. 3.6 shows that both BCBP1 and CBBP1 and their variants have strong serum stability revealed by SDS page. These proteins remain intact upon incubation with serum greater than 48 hours.
  • Embodiment of the PEGyation method of the present disclosure was applied to enhance the performance of developed contrast agents in imaging cancer biomarker.
  • Example 4 describes a novel protein-based MRI contrast agent for molecular targeting cancer marker HER2 has been developed by modification with pegylation.
  • the MRI contrast agent also carries a near-IR dye Cy5.5 for dual modality imaging of HER2 in cancer (Section 4.1).
  • Example 4 describes the development of a contrast agent that demonstrates specific interaction with HER2 positive cancer cells but not HER2 negative cells (4.2).
  • the in vitro MR imaging experiments with different cells that express different levels of HER2 have shown a close correlation between MRI contrast enhancements and HER2 levels (Section 4.3).
  • Example 4 describes that the MR imaging of xenograft models of human HER2 positive cell line SKOV3 and HER2 negative cell line MDA-MB-231 has indicated a HER2 level-dependent MRI contrast enhancement. This image intensity enhancement is further confirmed by NIR imaging (Section 4.4).
  • Example 4 describes immunohistochemical staining of tissue samples (including tumor tissue) collected after imaging analyses has shown that the designed contrast agent penetrated deep into the tumor mass (i.e., distant from tumor vasculature), demonstrating a good tissue penetration of the MRI contrast agent.
  • Differential targeting of the MRI contrast agent to HER2 positive and to HER2 negative tumors was further verified by immunoblot and ELISA analyses of the tissue samples collected from imaging mice (Section 4.5).
  • PEGylation of the designed Gd-binding protein not only increases protein solubility and blood circulation time, but also decreases immunogenicity of the protein without decrease of MRI relaxivity of the protein contrast agent. Therefore the designed HER2 targeting protein contrast agent was PEGylated using PEG-40, a PEG molecule with triple-branched 12 units PEG.
  • the resulting agent (PEG-CA1-Affi) exhibits very similar Gd 3+ binding properties and its T1 and T2 relaxivity values are similar to its parent protein CA1.CD2. Modifications did not change the overall protein fold as demonstrated by circular dichroism and fluorescence spectra.
  • AU565 is derived from breast carcinoma.
  • EMT6 is a mouse mammary tumor cell line.
  • AU565 cells express very high levels of HER2.
  • the EMT is regarded as a HER2 negative cell line.
  • Binding of the Gd-CA1.HER2/Affi to the cancer cells was first analyzed by immuno-fluorescence staining using a polyclonal antibody against PEGylated parental protein CA1.CD2 (PAbPGCA1). A substantial increase in staining intensities of CA1-Affi bound to AU565 cells was observed at both 37 and 4° C.
  • the protein did not bind to EMT6 cells.
  • CA1.CD2 without HER2 affibody did not bind to either of the tested cultured cells ( FIG. 4.2 ).
  • Proteins binding to cell surface HER2 with a clear membrane staining pattern in AU565 cells was observed at 4° C.
  • the binding of the proteins to the cells triggered receptor-mediated endocytosis at 37° C. as demonstrated by the staining of the protein inside the cells.
  • PEGylation of the targeted contrast agent PEG-CA1-Affi does not change its target capability the positive cell as shown in FIG. 4.2 at both 4 and 37° C.
  • Binding of the Gd-CA1-Affi to the cancer cells was further analyzed by quantification of cell bound Gd 3+ with AU565 and EMT6 cells.
  • the amounts of Gd 3+ were quantified by ⁇ -counting the trace of isotope 153 Gd 3+ in the Gd-protein complexes.
  • the quantification of cell bound Gd 3+ supported our immuno-analyses that Gd-CA1-Affi exhibited targeted binding to AU565 cells but not to EMT6 cells ( FIG. 4.3 ).
  • the protein without the HER2 affibody targeting moiety could not bind to the cells that express HER2.
  • mice were imaged using a Kodak in vivo FX-pro animal imaging system. Consistent with MRI imaging, we observed strong NIR light emission from both positive and negative tumor sites at early time points (50 minutes post-injection).
  • FIG. 4.4 shows the result of another mouse.
  • 5 mM of contrast agent CA1.Affi-P40 (100 fold lower than clinic used DTPA) was injected via tail vein.
  • MRI images at 4.7 T using fast spin echo were acquired before injection, 5 min, 30 min, 3 hr, 24 hr and 52 hr post injection.
  • Positive tumor shows a strong contrast after 30 mins and peaked at 24 hour with about 35% enhancement. Contrast capability was decreased after 52 hours, suggesting that the contrast agent was secreted of out the animal. This mouse was alive and looks normal after 52 hours MRI scanning.
  • Protein contrast agent Targeting of the protein contrast agent to HER2 positive tumor was further analyzed by immunoblot.
  • protein extracts were made from the tissue samples that were collected from the imaged mice. Immunoblot experiments were performed with the protein extracts using the antibody PAbPGCA1. Consistently, we detected very high levels of PEGylated protein contrast agent in extracts made from liver, kidney, and positive tumor. The antibody detected very faint bands in the extracts made from muscle and negative tumor samples ( FIG. 4.6 ). The results strongly suggested that our protein contrast agent led to a HER2 specific MR image enhancement.
  • CBP1-affi calmodulin
  • CBP1-Bom calmodulin
  • These targeted contrast agents were then PEGylated by PEG with different units and purified.
  • Initial binding to HER2 has been studied.
  • the HER2 positive cell line SKOV-3 and HER2 negative cell line MDA-MB-231 was treated with CBP1-affi at different concentration: 10 ⁇ M and 20 ⁇ M in 1 ml medium. Both of the cell numbers is about 1 ⁇ 10 5 .
  • FIG. 4.8 shows that the bands in SKOV-3 cells are much darker than those in MDA-MB-231 cells, which means the binding of CBP1-affi to HER2 is specific.
  • FIG. 4.9 shows the HER2 positive cell line SKOV-3 has been stained. The staining on the negative cell line is rarely.
  • FIG. 4.9 shows the uptake and internalization of CA1.Bom (CA1.CD2-52I-Bom) specifically to GRPR positive cell lines (PC-3 and DU-145 cells) by using confocal fluorescent microscope.
  • DU-145, PC-3 and H441 cells (8 ⁇ 10 4 ) were seeded in 4-well chambers (BD) at 37° C. overnight. In the second day, fresh medium was changed. Contrast agents were incubated with cells at different time point at 37° C. Subsequently, the cells were washed with PBS for three times and fixed with 3% formaldehyde for 15 minutes. After cells were rinsed in PBS for three times, 0.2% Triton X-100 was added to permeablize cells for 10 minutes. The cells were washed and four drops of Image-IT Fx signal enhancer (Invitrogen, CA) was applied in each sample to block unspecific binding. After three time washes, CD2 antibody was used as primary antibody. Goat anti-mouse IgG conjugated with Alexa Fluor 488 was used as detection antibody (Invitrogen, CA). The fluorescence image was acquired using 488 nm and UV lasers.
  • FIG. 4.11 shows NIR-fluorescence imaging of nude mice xenografted with DU-145 tumor (positive control left) and H441 tumor (control, right) post injection of CA1.CD2-52Ibom-cy5.5-P40 26 hours via tail vein. 50 uM Cy5-CA1.CD2-52I was injected into mouse tail vein. After 26 hours, mouse was analyzed by Kodak Imaging System. Tissue organs were taken out and analyzed. Tumor intensity was analyzed by Image J.
  • FIG. 4.12 shows NIR imaging (top) and NIR intensity (bottom) of CA1.CD2-52I-Bom-Cy5.5-P40 at different organs of the mice. The developed contrast agent is able to target to the GRPR expressed tumor monitored by NIR fluorescence.
  • ratios, concentrations, amounts, and other numerical data may be expressed herein in a range format. It is to be understood that such a range format is used for convenience and brevity, and thus, should be interpreted in a flexible manner to include not only the numerical values explicitly recited as the limits of the range, but also to include all the individual numerical values or sub-ranges encompassed within that range as if each numerical value and sub-range is explicitly recited.
  • a concentration range of “about 0.1% to 5%” should be interpreted to include not only the explicitly recited concentration of about 0.1 wt % to about 5 wt %, but also include individual concentrations (e.g., 1%, 2%, 3%, and 4%) and the sub-ranges (e.g., 0.5%, 1.1%, 2.2%, 3.3%, and 4.4%) within the indicated range.
  • the term “about” can include ⁇ 1%, ⁇ 2%, ⁇ 3%, ⁇ 4%, ⁇ 5%, ⁇ 6%, ⁇ 7%, ⁇ 8%, ⁇ 9%, or ⁇ 10%, or more of the numerical value(s) being modified.
  • the phrase “about ‘x’ to ‘y’” includes “about ‘x’ to about ‘y’”.
  • sequences are representative examples from protein families where sequences of the same protein across different species typically share 50-98% sequence homology.
  • attributes in the cited sequence can be inferred to apply to homologous, related sequences, which would be known to someone familiar with the art.
  • ADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGN 60 D93A ADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGN 60 D129A
  • ADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEV A ADGN 60 D20A ADQLTEEQIAEFKEAFSLF A KDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGN 60 Y99W (6)
  • Rat N-Calmodulin N-Terminal Domain of Calmodulin and Variants
  • N-CaM (11) ADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGN 60 N-N6OD (12) ADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGD 60 N-CaM GTIDFPEFLTMMARK 75 N-N6OD GTIDFPEFLTMMARK 75
  • Rat C-Calmodulin N-Terminal Domain of Calmodulin and Variants
  • ADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADDL 60 Mouse (18) ADQLTEEQIAEFKEAFSLFDKDGDNTITTKELGTVMRSLGQNPTEAELQDMINEVDAD-- 58 Rat (19) ADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDAD-- 58 Rabbit (20) ADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDAD-- 58 Paramecium (21) AEQLTEEQIAEFKEAFALFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDAD-- 58 Human PGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVEDKDGNGYISAAELRHVMTNLGEKLT 120 Mouse -GNGTIDFPEFLTMMARKM
  • CA1-WT (22) GSRDSGTVWGALGHGIELNIPNFQMTDDIDEVRWERGSTLVAEFKRKMKPFLKSGAFEID 60 CA1-Z HER2-4 (23) GSRDSGTVWGALGHGIELNIPNFQMTDDIDEVRWERGSTLVAEFKRKMKPFLKSGAFEID 60 CA1-Z HER342 (24) GSRDSGTVWGALGHGIELNIPNFQMTDDIDEVRWERGSTLVAEFKRKMKPFLKSGAFEID 60 CA1-WT ANGDLDIKNLTRDDSGTYNVTVYSTNGTRILNKALDLRILEGGSGGVDNKENKEQQNAFY 120 CA1-Z HER2-4 ANGDLDIKNLTRDDSGTYNVTVYSTNGTRILNKALDLRILEGGSGGVDNKFNKE LRQAYW 120 CA1-Z HER342 ANGDLDIKNLTRDDSGTYNVTVYSTNGTRILNKALDLRILEGGSGGVDNKFNKE MRNA

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US9187735B2 (en) 2012-06-01 2015-11-17 University Of Kansas Metal abstraction peptide with superoxide dismutase activity

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WO2009146099A2 (fr) 2009-12-03
US11738098B2 (en) 2023-08-29
EP2257316A4 (fr) 2014-10-22
US20210038745A1 (en) 2021-02-11
WO2009146099A3 (fr) 2010-02-18
EP2257316B1 (fr) 2018-11-07
US10849993B2 (en) 2020-12-01
EP3498307A1 (fr) 2019-06-19
US20240082434A1 (en) 2024-03-14
US20180250426A1 (en) 2018-09-06

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