Chemically Modifying Peptides
20170081360 ยท 2017-03-23
Inventors
Cpc classification
C07K1/1072
CHEMISTRY; METALLURGY
International classification
C07K1/107
CHEMISTRY; METALLURGY
Abstract
A method for chemically modifying a peptide, derivative or analogue thereof is described. The method comprises contacting a peptide, derivative or analogue thereof with a fluoro-heteroaromatic compound to activate the peptide, derivative or analogue thereof. The activated peptide, derivative or analogue thereof is then contacted with a nucleophile or base to create a chemically modified peptide, derivative or analogue thereof.
Claims
1. A method for chemically modifying a peptide, derivative or analogue thereof, the method comprising: (i) contacting a peptide, derivative or analogue thereof with a fluoro-heteroaromatic compound to activate the peptide, derivative or analogue thereof; and (ii) contacting the activated peptide, derivative or analogue thereof with a nucleophile or base to create a chemically modified peptide, derivative or analogue thereof.
2. The method according to claim 1, wherein the fluoro-heteroaromatic compound contains at least one nitrogen atom in its aromatic ring, and preferably contains one, two or three nitrogen atoms in the aromatic ring and/or the fluoro-heteroaromatic compound contains at least one fluorine atom, where the or each fluorine atom is covalently bonded to a carbon atom in the aromatic ring.
3. (canceled)
4. The method according to claim 1, wherein the fluoro-heteroaromatic compound comprises at least one hydrogen atom, wherein each hydrogen atom is covalently bonded to a carbon atom in the aromatic ring, or the fluoro-heteroaromatic compound comprises a perfluoroaromatic compound, or the fluoro-heteroaromatic compound comprises a chloro-fluoro-heteroaromatic compound.
5. (canceled)
6. (canceled)
7. The method according to claim 1, wherein the peptide, derivative or analogue thereof contains at least one nucleophilic side chain, preferably wherein the nucleophilic side chain reacts in an SNAr type reaction with the fluoro-heteroaromatic compound to displace a fluorine atom and create a covalent bond between the nucleophilic side chain and the heteroaromatic compound.
8. (canceled)
9. The method according to claim 7, wherein the peptide or derivative or analogue thereof is activated in step (i) due to the formation of a leaving group on the peptide, derivative or analogue thereof, preferably wherein the leaving group comprises the heteroaromatic compound, which is covalently bonded to the nucleophilic side chain, and at least a portion of the nucleophilic side chain.
10. The method according to claim 1, wherein step (i) of the method comprises dissolving a peptide, derivative or analogue thereof in a solvent, which is preferably 2,2,2-trifluoroethanol (TFE), and adding a base, which is preferably N,N-diisopropylethylamine (DIPEA), thereto before the fluoro-heteroaromatic compound is added to the dissolved peptide to create a reaction solution.
11. (canceled)
12. The method according to claim 10, wherein the molar ratio of the peptide, derivative or analogue thereof to the fluoro-heteroaromatic compound in step (i) is between 1:1 and 1:100, or between 1:5 and 1:50, or between 1:10 and 1:40, or between 1:20 and 1:30 and/or the molar ratio of the activated peptide, derivative or analogue thereof to the nucleophile or base in step (ii) is between 1:1 and 1:100, or between 1:5 and 1:10, or between 1:10 and 1:40, or between 1:20 and 1:30.
13. The method according to claim 1, wherein step (ii) of the method comprises contacting the activated peptide, derivative or analogue thereof with a nucleophile, wherein the nucleophile displaces the leaving group and creates a covalent bond between the peptide, derivative or analogue thereof and the nucleophile.
14. The method according to claim 1, wherein the method comprises contacting the activated peptide, derivative or analogue thereof with at least two nucleophilic molecules and the nucleophilic molecules displace two or more halogens on the heteroaromatic compound.
15. The method according to claim 1, wherein the nucleophile: a) comprises an organic molecule possessing nucleophilic functionality; and/or b) includes at least one group possessing nucleophilic functionality which is selected from a thiol group, a hydroxyl group, a primary amine group, a secondary amine group and a selenol group; and/or c) is selected from a group consisting of: a thiol containing sugar, a thiol containing nucleoside, a thiol containing alkyl chain, a thiol containing PEGylating agent, a thiol containing fluorescent tag, a thiol containing antibody, a hydroxyl containing sugar, a hydroxyl containing nucleoside, a hydroxyl containing alkyl chain, a hydroxyl containing PEGylating agent, a hydroxyl containing fluorescent tag, a hydroxyl containing antibody, an amine containing sugar, an amine containing nucleoside, an amine containing alkyl chain, an amine containing PEGylating agent, an amine containing fluorescent tag, an amine containing antibody, a selenol group the nucleophile may comprise a selenol containing sugar, a selenol containing nucleoside, a selenol containing alkyl chain, a selenol containing PEGylating agent, a selenol containing fluorescent tag and a selenol containing antibody; and/or d) is glutathione.
16. (canceled)
17. (canceled)
18. (canceled)
19. The method according to claim 1, wherein the chemical modification comprises conjugation of a chemical entity onto the peptide, preferably wherein the chemical entity is selected from a group consisting of a sugar, preferably a thiosugar, a nucleoside, an alkyl chain, PEG, a fluorescent tag and an antibody.
20. The method according to claim 1, wherein the method, step (ii) comprises contacting the activated peptide, derivative or analogue thereof with a base, preferably wherein the base is potassium thioacetate, and wherein the activated peptide, derivative or analogue thereof undergoes an elimination reaction resulting in the formation of a dehydroalanine-containing peptide, derivative or analogue thereof.
21. (canceled)
22. (canceled)
23. The method according to claim 20, wherein an additional step is carried out, subsequent to step (ii), the step comprising further reacting the dehydroalanine-containing peptide, derivative or analogue thereof to attach a chemical entity to the peptide, preferably wherein the chemical entity is selected from a group consisting of a sugar, preferably a thiosugar, a nucleoside, an alkyl chain, PEG, a fluorescent tag and an antibody.
24. (canceled)
25. The method according to claim 7, wherein at least one of the nucleophilic side chains comprises an amine group, wherein the amine group preferably comprises a primary amine or secondary amine, preferably wherein the or each amine group is provided on an amino acid residue within the peptide, derivative or analogue thereof, and preferably the or each amine group is provided on a lysine residue in the peptide, derivative or analogue thereof.
26. (canceled)
27. The method according to claim 7, wherein at least one of the nucleophilic side chains preferably comprises a thiol group, preferably wherein the or each thiol is provided on a cysteine residue or modified cysteine residue in the peptide, derivative or analogue thereof.
28. The method according to claim 7, wherein at least one of the nucleophilic side chains preferably comprises an alcohol group, preferably wherein the alcohol group preferably comprises a phenol group, and preferably wherein the or each alcohol group is provided on a serine or threonine residue within the peptide, derivative or analogue thereof
29. The method according to claim 7, wherein at least one of the nucleophilic side chains preferably comprises a selenol group, preferably wherein the or each selenol group may be provided on a selenocysteine residue within the peptide, derivative or analogue thereof.
30. (canceled)
31. (canceled)
32. A chemically modified peptide, derivative or analogue thereof obtained or obtainable by the method according to claim 1.
33. A chemically modified peptide, derivative or analogue thereof according to claim 32, wherein the chemically modified peptide, derivative or analogue thereof is functionalised or tagged with a selected chemical entity, preferably wherein the chemical entity is selected from a group consisting of a sugar, preferably a thiosugar, a nucleoside, an alkyl chain, PEG, a fluorescent tag and an antibody.
34. A dehydroalanine-containing peptide, derivative or analogue thereof, the dehydroalanine-containing peptide, derivative or analogue thereof obtained by the method according to claim 1.
35. (canceled)
36. (canceled)
Description
[0085] For a better understanding of the invention, and to show how embodiments of the same may be carried into effect, reference will now be made, by way of example, to the accompanying Figures, in which:
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EXAMPLES
[0105] As mentioned previously, it is desirable to be able to chemically modify peptides, analogues and derivatives thereof. It is often desirable to chemically modify a peptide, analogue or derivative thereof by attaching a chemical entity to the said peptide, analogue or derivative thereof. Much work has been done in developing this process in the prior art.
[0106] One method developed in the prior art involves linking the peptide, analogue or derivative thereof to the chemical entity by means of a linker. A schematic showing how this can be achieved is shown in
[0107] Alternatively, the Davis group at Oxford have devised an approach that results in a disulfide linkage being present in the final product, as shown in
[0108] The applicant has developed a new technology platform that allows chemical moieties to be attached to a peptide or protein in a manner that does not involve a linker.
[0109] An alternative embodiment of the present invention allows the formation of dehydroalanine intermediates by a novel method. A schematic illustrating this embodiment is shown in
[0110] The applicant has also developed a new technology platform that allows multiple chemical moieties to be attached to a peptide or protein.
[0111] Materials and Methods
[0112] Five different peptides, referred to as peptides 1 to 4, were prepared where:
[0113] Peptide 1 has the structure AcNH-Y-C-G-G-G-C-A-L-CONH.sub.2;
[0114] Peptide 2 has the structure AcNH-A-C-Y-G-S-I-L-A-R-T-CONH.sub.2;
[0115] Peptide 3 has the structure AcNH-F-C-G-G-G-C-A-L-CONH.sub.2; and
[0116] Peptide 4 has the structure AcNH-F-S-G-G-G-S-A-L-CONH.sub.2;
[0117] Peptides 1-4 was prepared using automated Fmoc-SPPS methods on a Liberty 1 peptide synthesizer (CEM) with microwave-assisted couplings (single coupling per amino acid; 10 min, 75 C. (50 C. for Fmoc-cys(trt)-OH coupling). Solid phase synthesis was conducted using Rink amide resin (0.7 mol/g loading) on a 0.1 mol scale, employing PyBOP and DIPEA as activator and base, respectively. Following on-resin synthesis of the appropriate sequence, N-terminal capping was achieved using Ac.sub.2O/DMF (20%, 215 min) with shaking at room temperature. Finally, peptides were cleaved from the resin as the C-terminal amide by treatment of beads with a cleavage cocktail containing 90% TFA, 5% TIPS and 5% water with shaking at room temperature for 4 h. After removal of volatiles in vacuo, the product was triturated and washed using Et.sub.2O.
[0118] The structures of the fluoro-heteroaromatics and fluoro-aromatic used are shown in
[0119] The peptides were reacted according to procedures A and B as described below:
[0120] Procedure A
[0121] Solid peptide (approx. 2 mg, 2.5 mol) was dissolved in DMF (0.5 mL) in a 1.5 mL plastic Eppendorf tube, to which DIPEA (50 mM in DMF, 0.5 mL) was added. The fluoro-heteroaromatic or fluoroaromatic was then added in 25 equivalents and the tube was shaken at room temperature for 4.5 h. After removal of volatiles under vacuum, each reaction mixture was re-dissolved in a 1:1 mixture of H.sub.2O and MeCN (1 mL) and analyzed by LCMS (ESI+).
[0122] Procedure B
[0123] Solid peptide (approx. 2 mg, 2.5 mol) was dissolved in TFE (0.5 mL) in a 1.5 mL plastic Eppendorf tube, to which DIPEA (50 mM in TFE, 0.5 mL) was added. The fluoro-heteroaromatic or fluoroaromatic was added in 25 equivalents and the tube was shaken at room temperature for 4.5 h. After removal of volatiles under vacuum, each reaction mixture was re-dissolved in a 1:1 mixture of H.sub.2O and MeCN (1 mL) and analyzed by LCMS (ESI+) and .sup.19F NMR (100 L D.sub.2O added).
[0124] Procedure C
[0125] DIPEA (20 L) was added to a solution of peptide (0.3 mg) in MeCN (0.5 mL) and water (0.5 mL) in a 1.5 mL plastic Eppendorf tube. A sulphur nucleophile was added in 5 equivalents and the tube was shaken at room temperature for 4 h and then analyzed by LCMS (ESI+).
[0126] The inventor has found that when the reagents are reacted according to procedure B the fluoro-heteroaromatic selectively reacts with cysteine residues instead of the tyrosine residues.
[0127] LC-MS Conditions:
[0128] Peptides and peptoids were characterised by LC-MS, ESI-LC MeCN (TQD mass spectrometer and an Acquity UPLC from Waters) using an Acquity UPLC BEH C8 1.7 m (2.1 mm50 mm) column and (C18 as of Jun. 2, 2015 3 pm) with a flow rate of 0.6 ml min.sup.1, a linear gradient of 5-95% of solvent B over 3.8 min (A=0.1% formic acid in H.sub.2O, B=0.1% formic acid in MeCN) and injection volume of 1 l.
[0129] QToF (mass spectrometer and an Acquity UPLC from Waters) using an Acquity UPLC BEH C8 1.7 m (2.1 mm50 mm) column with a flow rate of 0.6 ml min.sup.1, a linear gradient of 0-99% of solvent B over 5 min (A=0.1% formic acid in H.sub.2O, B=0.1% formic acid in MeCN) and injection volume of 3 l.
[0130] Peptides and peptoids identities were also confirmed by MALDI-TOF mass spectra analysis (Autoflex II ToF/ToF mass spectrometer Bruker Daltonik GmBH) operating in positive ion mode using an -cyano-4-hydroxycinnamic acid (CHCA or CHHA) matrix. Data processing was done with MestReNova Version 10.0.
[0131] TQD
[0132] ESI-LC MeCN (TQD): Acquity UPLC BEH C8 1.7 m (2.1 mm50 mm) (C18 as of Jun. 2, 2015 3 pm)
[0133] Mobile phase: water containing formic acid (0.1% v/v):Acetonitrile
[0134] Flow rate 0.6 ml min.sup.1
[0135] Injection volume: 1 l
[0136] Gradient:
TABLE-US-00001 Time (min) % A % B 0 95 5 0.2 95 5 4 5 95 4.5 5 95 5 95 5
[0137] Data processing: MestReNova 10.0
[0138] QToF
[0139] Accurate mass: Acquity UPLC BEH C18 1.7 m (2.1 mm100 mm)
[0140] Mobile phase: water containing formic acid (0.1% v/v):Acetonitrile
[0141] Flow rate: 0.6 ml min.sup.1
[0142] Injection volume: 3 l
[0143] Gradient:
TABLE-US-00002 Time (min) % A % B 0 100 0 5 1 99 6 1 99 6.1 100 0 7 100 0
[0144] Data processing: MestReNova 10.0
[0145] MALDI
[0146] Autoflex II ToF/ToF mass spectrometer Bruker Daltonik GmBH 337 nm nitrogen laser
[0147] Sample preparation 1 mg/ml, 1 l spotted on matrix
[0148] Operating in positive ion mode using an -cyano-4-hydroxycinnamic acid (CHCA or HCCA) matrix
[0149] Data acquisition: reflecton mode of analysis
[0150] Data processing: MestReNova 10.0
Example 1
Reacting Peptides 1 to 4 with Fluoro-Heteroaromatic or Fluoroaromatic Compounds to Obtain Activated Peptides
[0151] Peptides 1 to 4 were further reacted using either procedure A or procedure B to create a stock of modified peptides, as set out in table 1.
TABLE-US-00003 TABLE 1 Reaction of peptides 1 to 4 according to procedure A or B LCMS Fluoro- spectrum and Peptide heteroaromatic chromatogram Product 1*
[0152] It will be readily appreciated that while a selection of fluoro-heteroaromatic compounds were used in this instance many more fluoro-heteroaromatic compounds could be used to create a peptide with a suitable leaving group.
Example 2
Reaction of Peptide 6 with Thiophenolate
[0153] Peptide 6 was reacted with thiophenolate according to the following reaction procedure:
[0154] To a solution of Peptide 6 (2 mg, 1.8 mol) in MeCN (0.5 mL) and water (0.5 mL) in a 1.5 mL plastic Eppendorf tube, was added DIPEA (20 L). Sodium thiophenolate was added in 5 equivalents and the tube was shaken at room temperature for 4 h and then analyzed by LCMS (ESI+).
[0155] An LCMS spectrum of the crude reaction mixture is shown in
[0156]
[0157] Accordingly, one embodiment of the present invention is a method for attaching a chemical moiety to a peptide or protein in a manner that does not involve a linker.
Example 3
Reaction of Peptide 6 with Thioacetate
[0158] Peptide 6 was reacted with potassium thioacetate according to the following reaction procedure:
[0159] To a solution of Peptide 6 (2 mg, 1.8 mol) in MeCN (0.5 mL) and water (0.5 mL) in a 1.5 mL plastic Eppendorf tube, was added DIPEA (20 L). Potassium thioacetate was added in 5 equivalents and the tube was shaken at room temperature for 4 h and then analyzed by LCMS (ESI+).
[0160] An LCMS spectrum of the crude reaction mixture is shown in
[0161]
[0162] Accordingly, an alternative embodiment of the present invention is a new method enabling the creation of dehydroalanine containing peptides. The general approach for this is shown in
Example 4
Further Reaction of Activated Peptides with Sulphur Nucleophiles
[0163] The activated peptides obtained by reacting peptide 2 with various fluoroheteroaromatic compounds in Example 1 were further reacted with various sulphur nucleophiles according to Procedure C.
TABLE-US-00004 TABLE 2 Reaction of Peptides 6, 8, 9, 10, 11a and 11b with sulphur nucleophiles according to procedure C Sulphur Peptide Nucleophile Product 6
[0164] When peptide 6 was exposed to sodium thiophenolate, the sulphur nucleophile displaced two heteroaromatic groups on peptide 6 to give product 201. This results in original peptide 2 having been tagged, without using a linker, at a cysteine residue and a serine residue.
[0165] Similarly, when peptides 8, 10 and 11a were reacted with sodium thiophenolate peptide 8 reacted to give product 202, peptide lo reacted to give product 206, and peptide 11a reacted to give product 207, all of which have undergone a displacement reaction. This results in original peptide 2 having been tagged, without using a linker, at a cysteine residue.
[0166] For the aforementioned reactions the peptides underwent displacement reactions but the heteroaromatic group attached on the tyrosine resides were unreacted. Accordingly, the inventors have shown that it is possible to selectively tag molecules at chosen residues (i.e. cysteine or serine) in the presence of an activated tyrosine residue. Additionally, the inventors have shown that sometimes instead of displacing a heteroaromatic group the sulphur nucleophile instead displaces one or more of the halogens on the aromatic ring. Due to the presence of multiple halogens on the ring, it is possible to add multiple tags to a heteroaromatic group. An example of this is where peptide 11a reacted with sodium thiophenolate to give the product 207. An example of displacing only one halogen can be seen in the reaction between peptide 9 and the nucleophile 1-Thio--D-glucose tetraacetate which affords the product 205.
Example 5
Further Reaction of Activated Peptides with Sulphur Nucleophiles
[0167] The activated peptides obtained by reacting peptide 3 with various fluoroheteroaromatic compounds in Example 1 were further reacted with various sulphur nucleophiles according to Procedure C.
TABLE-US-00005 TABLE 3 Reaction of Peptides 12 and 14b with sulphur nucleophiles according to procedure C Sulphur Peptide(s) Nucleophile Product 12
[0168] When peptide 12 was exposed to 1-thio--D-glucose tetraacetate, the sulphur nucleophile displaced one of the fluorine atoms on the fluoro-heteroaromatic bridge to give product 301. Similarly when peptide 14b was exposed to 1-thio--D-glucose tetraacetate, the sulphur nucleophile displaced on of the fluorine atoms on the fluoro-heteroaromatic bridge to give product 302. This demonstrates that it is possible to tag a fluoro-heteroaromatic containing cyclic peptides without causing degradation of the cyclic peptide. This approach offers a novel route to prepare tagged cyclic peptides.
[0169] It should be noted that when peptide 3 was modified using a hexafluorobenzene , to give peptide 19, the inventors found that this modified peptide did not react with the sulphur nucleophile to give a tagged cyclic product. This highlights the advantage over the prior art afforded through the application of a perfluoro-heteroaromatic reagent to activate the peptides.
Example 6
Further Reaction of Activated Peptides with Sulphur Nucleophiles
[0170] The activated peptides obtained by reacting peptide 4 with various fluoroheteroaromatic compounds in Example 1 were further reacted with various sulphur nucleophiles according to Procedure C.
TABLE-US-00006 TABLE 4 Reaction of Peptides 22a, 22b, 23a and 27b with sulphur nucleophiles according to procedure C Sulphur Peptide Nucleophile Product 22a and 22b
[0171] When peptide 22b was exposed to 1-thio--D-glucose tetraacetate, the sulphur nucleophile displaced one heteroaromatic group on peptide 22b to give product 402. This results in original peptide 4 having been tagged, without using a linker, at a serine residue.
[0172] When peptide 23a was exposed to 1-thio--D-glucose tetraacetate, the sulphur nucleophile displaced one heteroaromatic group on peptide 23a to give product 405. This results in original peptide 4 having been tagged, without using a linker, at a serine residue.
[0173] Additionally peptide 22ba reacted with 1-thio--D-glucose tetraacetate to give the product 403, where the sulphur nucleophile displaced two halogens on each aromatic ring, thereby adding multiple tags to the heteroaromatic group. Further examples of this include where peptide 23a reacted with sodium thiophenolate to give the multiply tagged product 404 and where peptide 27b reacted with sodium thiophenolate to give the multiply tagged product 406.
SUMMARY
[0174] Advantages of the invention include the possibility of chemically modifying activated peptides under mild conditions in a traceless fashion. Traceless chemical modification is not currently available through other published methodologies most of which require the use of a linker moiety being present in the final product. The methodology requires peptide activation via reaction with a halogenated heteroaromatic followed by nucleophilic displacement of the halogenated heteroaromatic. Selectivity between serine/cysteine activated residues and tyrosine activated residues has been demonstrated. Nucleophilic displacement occurs directly without the need to install a dehydro-alanine type motif which in other published methodologies leads to the loss of stereo-chemical integrity.
[0175] However, if the installation of a dehydro-alanine type motif is desired, the activated peptide can be reacted under mild conditions to install the motif into the peptide backbone.
[0176] Activation of a peptide through a halogenated heteroaromatic has also been shown to offer a route to attach multiple chemical moieties to a linear or cyclic peptide. The aforementioned reaction has been shown not to be possible if carried out with a published halogenated aromatic (e.g. hexafluorobenzene) activated peptide.