# Patent

## Title
Aminoglycoside-polyamine displacers and methods of use in displacement chromatography

## Abstract

Aminoglycoside-polyamines are disclosed along with methods of use thereof in displacement chromatography and as DNA-binding ligands. The aminoglycoside-polyamines are derivatives of carbohydrates, such as sugars, amino sugars, deoxysugars, glycosides, nucleosides and their substituted counterparts. The subject polyamines possess a




group in place of at least one hydrogen atom of at least one hydroxyl group of the carbohydrate compound. In these compounds R1 is an alkyl group or an azaalkyl group, and R2 is a primary or secondary amino group.

## Background
FEDERALLY SPONSORED RESEARCH
The following invention was made with Government support under contract number 0079436 awarded by the National Science Foundation and contract number GM047372 awarded by the National Institutes of Health. The Government has certain rights in this invention.


FIELD OF THE INVENTION
The invention relates to aminoglycoside-polyamines, and methods of use thereof in displacement chromatography and as DNA-binding ligands.
BACKGROUND OF THE INVENTION
Displacement chromatography has attracted significant attention as a powerful technique for the purification of biotherapeutic proteins and oligonucleotides. In particular, low molecular weight (MW<2000) displacers have been shown to have significant advantages for high-resolution protein purification. Displacement chromatography enables simultaneous concentration and purification in a single step, which is significant in the purification of biopharmaceuticals. However, the major obstacle in implementing this technique is the lack of a sufficient diversity of appropriate displacer candidates that are applicable across a wide spectrum of bioseparation demands. Low molecular weight displacers employed to date possess moderate to high affinities, yet are unable to displace highly retained proteins on a variety of hydrophilic and hydrophobic resins. Thus, a need exists to develop high affinity and selective displacers that overcome at least one of the aforementioned deficiencies.
SUMMARY OF THE INVENTION
An aspect of the present invention relates to a derivative of a carbohydrate compound selected from a sugar, an amino sugar, a deoxysugar, a glycoside, a nucleoside, a substituted sugar, a substituted amino sugar, a substituted glycoside, a substituted aminoglycoside, and a substituted nucleoside, said derivative comprising: a group of formula I




in place of at least one hydrogen atom of at least one hydroxyl group of the carbohydrate compound, or, when present, of at least one amino group of the carbohydrate compound wherein R1 is an alkyl group or an azaalkyl group, and R2 is a primary or secondary amino group.

A second aspect of the present invention is a method for separating one or more components of a biomolecule mixture by means of an ion exchange chromatographic system operated in the displacement mode, said method comprising: sequentially perfusing the system with a first solution comprising the biomolecule mixture, and a second solution comprising a derivative of a carbohydrate compound of formula 1 described above.
A third aspect of the present invention is a method for separating a protein or peptide mixture by means of an ion exchange chromatographic system operated in the displacement mode, said method comprising: sequentially perfusing the system with a first solution comprising said mixture, and a second solution comprising a derivative of a carbohydrate compound of formula 1.
A fourth aspect of the present invention is a method for condensing DNA, said method comprising: combining DNA with at least one derivative of a carbohydrate compound of formula 1 as described above, wherein the DNA is bound to the derivative of the carbohydrate compound.



BRIEF DESCRIPTION OF THE DRAWINGS
FIG. 1 depicts a graph for the displacement of cytochrome-C by various concentrations of neamine and its derivatives, in accordance with the present invention;
FIG. 2 depicts a graph comparing the % lysozyme and % cytochrome-C displaced on HP Sepharose SP, in accordance with the present invention; and
FIG. 3 depicts a graph of DNA binding efficacy of the displacer candidates, in an embodiment of the present invention.



DETAILED DESCRIPTION OF THE INVENTION
Definitions
Throughout this specification the terms and substituents retain their definitions.
The term alkyl is intended to include a linear, a branched, or a cyclic hydrocarbon structure, and combinations thereof. A lower alkyl refers to alkyl groups having from about 1 to about 4 carbon atoms. Examples of lower alkyl groups include but are not limited to methyl, ethyl, n-propyl, isopropyl, and n-, s- and t-butyl, and the like. A cycloalkyl is a subset of alkyl and includes cyclic hydrocarbon groups having from about 3 to about 8 carbon atoms. Examples of cycloalkyl groups include but are not limited to cyclopropyl, cyclobutyl, cyclopentyl, norbornyl, and the like. Typical alkyl groups are those of C20 or below in an embodiment of the present invention.
Examples of a C1 to C20 hydrocarbon include but are not limited to alkyl, cycloalkyl, alkenyl, alkynyl, aryl and combinations thereof. Examples include benzyl, phenethyl, cyclohexylmethyl, camphoryl and naphthylethyl. The term “phenylene” refers to ortho, meta or para residues of the formulae:




Polyol refers to a compound or residue having a plurality of —OH groups. Polyols may be thought of as alkyls in which a plurality of C—H bonds have been replaced by C—OH bonds. Common polyol compounds include for example glycerol, erythritol, sorbitol, xylitol, mannitol and inositol. Linear polyol residues will generally be of the empirical formula —CyH2y+1Oy, and cyclic polyol residues will generally be of the formula —CyH2y−1Oy. Cyclic polyols also include reduced sugars, such as glucitol.
Alkoxy or alkoxyl refers to groups having from about 1 to about 8 carbon atoms of a straight, branched, or cyclic configuration, and combinations thereof attached to the parent structure through an oxygen atom. Examples include but are not limited to methoxy, ethoxy, propoxy, isopropoxy, cyclopropyloxy, cyclohexyloxy and the like. Lower alkoxy refers to groups from about 1 to about 4 carbon atoms of a straight, branched, cyclic configuration, and combinations thereof attached to the parent structure through an oxygen atom.
Oxaalkyl refers to an alkyl residue in which one or more carbons (and their associated hydrogens) have been replaced by oxygen. Examples include methoxypropoxy, 3,6,9-trioxadecyl and the like. The term oxaalkyl is intended as it is understood in the art [see Namina and Indexina of Chemical Substances for Chemical Abstracts, published by the American Chemical Society, 1[196, but without the restriction of 1 [127(a)], i.e. it refers to compounds in which the oxygen is bonded via a single bond to its adjacent atoms (forming ether bonds); it does not refer to doubly bonded oxygen, as would be found in carbonyl groups. Similarly, thiaalkyl and azaalkyl refer to alkyl residues in which one or more carbons has been replaced by sulfur or nitrogen, respectively. Examples include ethylaminoethyl and methylthiopropyl.
Acyl refers to a group having from about 1 to about 8 carbon atoms of a straight, branched, or cyclic configuration being saturated, unsaturated, or aromatic and combinations thereof, attached to the parent structure through a carbonyl functionality. One or more carbons in the acyl group may be replaced by nitrogen, oxygen or sulfur as long as the point of attachment to the parent remains at the carbonyl. Examples include acetyl, benzoyl, propionyl, isobutyryl, t-butoxycarbonyl, and benzyloxycarbonyl. Lower-acyl refers to groups containing one to four carbons.
Aryl and heteroaryl refers to a 5- or 6-membered aromatic or heteroaromatic ring containing 0-3 heteroatoms selected from nitrogen, oxygen or sulfur; a bicyclic 9- or 10-membered aromatic or heteroaromatic ring system containing 0-3 heteroatoms selected from nitrogen, oxygen or sulfur; or a tricyclic 13- or 14-membered aromatic, or heteroaromatic ring system containing 0-3 heteroatoms selected from nitrogen, oxygen or sulfur.
Examples of aromatic 6- to 14-membered carbocyclic rings include but are not limited to benzene, naphthalene, indane, tetralin, fluorine, and the like. Examples of 5- to 10-membered aromatic heterocyclic rings include but are not limited to imidazole, pyridine, indole, thiophene, benzopyranone, thiazole, furan, benzimidazole, quinoline, isoquinoline, quinoxaline, pyrimidine, pyrazine, tetrazole, pyrazole, and the like.
An arylalkyl means an alkyl residue attached an aryl ring. Examples include but are not limited to benzyl, phenethyl, and the like. Heteroarylalkyl means an alkyl group attached to a heteroaryl ring. Examples include but are not limited to pyridinylmethyl, pyrimidinylethyl, and the like. Alkylaryl means an aryl structure having one or more alkyl groups attached thereto. Examples include but are not limited to tolyl, mesityl, and the like.
Heterocycle refers to a cyclic structure or residue in which one or more of the ring atoms are replaced by an atom other than carbon. Examples include of a replacement atom includes but are not limited to oxygen, nitrogen, sulfur, and the like. Examples of heterocycles that fall within the scope of the invention include but are not limited to pyrrolidine, pyrazole, pyrrole, indole, quinoline, isoquinoline, tetrahydroisoquinoline, benzofuran, benzodioxan, benzodioxole (commonly referred to as methylenedioxyphenyl, when occurring as a substituent), tetrazole, morpholine, thiazole, pyridine, pyridazine, pyrimidine, thiophene, furan, oxazole, oxazoline, isoxazole, dioxane, tetrahydrofuran, and the like.
Haloalkyl refers to an alkyl residue, wherein a halogen atom replaces one or more H atoms. Examples of a haloalkyl group include but are not limited to —CH2F, —CHF2, —CF3, and the like.
Substituted refers to an alkyl, an alkoxy or alkoxyl, an oxaalkyl, an acyl, an arylalkyl, a heterocycle, a haloalkyl, or a carbohydrate, wherein one or more H atoms of the aforementioned groups or the carbohydrate is replaced with an alkyl, an alkoxy or alkoxyl, an oxaalkyl, an acyl, an arylalkyl, a heterocycle, a haloalkyl, an alkynyl, a carbonyl, a carboxy, a carboxalkoxy, a carboxamido, an acyloxy, an amidino, a nitro, a halogen, a hydroxy, an OCH(COOH)2, a cyano, an amino group, an acylamino, an alkylthio, a sulfoxide, a sulfone, and the like. Examples of the substituted group, i.e. substituent, include but are not limited to phenyl, benzyl, methoxy, acetoxy, acetyl, phenoxy, and benzyloxy. Typically, an acyl, alkoxy or aryloxy group, such as OAc, OBz, or OPh, may replace one or more OH groups of the carbohydrate compound.
The term “sugar” as used in the context of the current invention is defined as listed in Hawley's Condensed Chemical Dictionary, 12th Edition, Richard J. Lewis, Sr.; Van Nostrand Reinhold Co. New York. The definition encompasses any carbohydrate comprised of one or two saccharose groups. Monosaccharide sugars (often called simple sugars) are composed of chains of 2-7 carbon atoms. One of the carbon atoms carries an aldehydic or ketonic oxygen, which may be combined in acetal or ketal forms. The remaining carbons usually have hydrogen atoms and hydroxyl groups. Unless specifically noted otherwise, the term “sugar” refers to both D-sugars and L-sugars.
Examples of a sugar include but are not limited to ribose, xylose, ribulose, xylulose, deoxyribose, galactose, glucose, mannose, fructose, sorbose, tagatose, fucose, quinovose, rhamnose, manno-heptulose, sedoheptulose, sucrose, lactose, maltose, cellobiose, galactose, lactose, xylose, arabinose, celloboise, maltose, raffinose, rhamnose, melibiose, ribose, fucose, lyxose, and the like.
An amino sugar or glycosamine is defined as a sugar derivative having an amino group in place of one of the primary or secondary hydroxyls of the sugar. Examples of an amino sugar include but are not limited to glucosamine, galactosamine, mannosamine, and the like.
A sugar alcohol, also known as a polyol, polyhydridic alcohol, or polyalcohol, is a hydrated form of a carbohydrate whose carbonyl group (aldehyde or ketone) has been reduced to a primary or secondary hydroxyl group. Examples of a sugar alcohol include but are not limited to an acyclic polyol such as an alditol or a glycitol, erythritol, sorbitol, mannitol, adonitol, arabitol, zylitol, dulcitol, myo-insoitol, and the like. Further, cyclitols are class of sugar alcohols that are comprised of cycloalkanes containing one hydroxyl group on each of three or more ring atoms.
A deoxysugar is any sugar containing fewer oxygen atoms than carbon atoms, resulting in one or more carbon atoms of the molecule lacking an attached hydroxyl group. See the American Heritage® Stedman's Medical Dictionary, 2nd edition, Copyright © 2004 by Houghton Mifflin Company.
Glycosides are acetal derivatives of the cyclic forms of sugars in which the hydrogens of the hemiacetal hydroxyls have been replaced by alkyl or aryl groups, where R is alkyl, aryl, alkylaryl, arylalkyl, substituted alkyl, substituted aryl, substituted alkylaryl, substituted arylalkyl, haloalkyl, alkoxy, aryloxy, heteroaryl, heteroaryloxy, monosaccaride, oligosaccharide, and the like. Examples of an OR replacement group include but are not limited to methoxy, acetoxy, acetyl, phenoxy, or benzyloxy. Preferably, the aglycone component of the glycoside (glycone) may be alkyl or aryl.
An aminoglycoside belongs to a group of antibiotics, which contain a sugar bonded to an amino (NH2) group. Examples include but are not limited to amikacin (Also known as BB-K8), Butirosin A & B, Geneticin, Gentamicin A, Kanamycin A & B (about 5% Kanamycin B), Lividomycin A, Neomycin B & C (about 15% Neomycin C), Paromomycin I & II, 6′-N-Methylamikacin, 4′-Deoxy-6′N-Methylamikacin, Butikacin (Also known as Butakacin), 5′′-Amino-5′′-Deoxybutirosin A, 1-N-HAPA-Gentamicin B, Gentamicin B, Hybrimycin A1, Hybrimycin A2, Hybrimycin B1, Hybrimycin B2, Kanamycin C, 4,6-di-O-(6-amino-6-deoxy-α-D-glucopyranosyl)-2-deoxystreptamine, 4-O-(6-amino-6-deoxy-.alpha.-D-glucopyranosyl)-6-O-(α-D-glucopyranosyl)-2-deoxystreptamine, 6′-N-methylkanamycin, 6′′-Chloro-6′′-deoxykanamycin, 6′′-Deoxykanamycin A, Kanamycin-6′′-uronic acid, Kanamycin-6′′-phosphate, 6′′-Amino-6′′-deoxykanamycin, 6′′-Hydrazino-6′′-deoxykanamycin, Tetrakis-N-(p-chlorobenzyl)kanamycin, 4′′,6′′-O-benzylidenekanamycin, 2′′-manno-kanamycin, 6′′-amino-6′′-deoxy-2′′-manno-kannamycin, 6′′-deoxy-6′′-hydrazino-2′′-manno-kanamycin, Lividomycin B, Neomycin A (Also known as Neamine), Propikacin (Also known as UK 31214), and the like.
Further examples of an aminoglycoside include but are not limited to Ribostamycin, Ribostamycin-5′′-uronic acid, Seldomycin 5, 3-N-Acetylseldomycin 5, 3′-Episeldomycin 5, 6′-N-Methylseldomycin 5, 1-N-HABA-Seldomycin 5, 1 -N-Ethylseldomycin 5, Trehalosamine, α-D-mannosyl-α-D-glucosaminide, Apramycin (Also known as Nebramycin), Bluensomycin (Also known as Glebomycin), Gentamicin C1, Gentamicin C2, Gentamicin C1a, Gentamicin C2b (Also known as Sagamicin), 3′,4′-unsaturated kanamycin B, 3′,4′-dideoxy-6′-N-methylkanamycin B, 3′-amino-3′-deoxy-2′-manno-kanamycin, 3′-amino-3′-deoxykanamycin, Netromycin (Also known as netilmicin), 3′,4′-dideoxyribostamycin, 3′, 4′, 5′′-trideoxyribostamycin, 3′-Deoxyseldomycin 5, Streptomycin, Dihydrostreptomycin, Dihydrodeoxystreptomycin, Hydroxystreptomycin, N-demethylstreptomycin, Mannosidostreptomycin, Tobramycin (Also known as nebramycin factor 6), Sisomicin, G-52 (Also known as 6′-N-methylsisomicin), Verdamicin (Also known as 6′-C-methylsisomicin), Destomycin A, Antibiotic A-396-I, Dibekacin, HABA-dibekacin, HABA-methyldibekacin, Kasugamycin, Fortimicin A, 5-episisomicin, aminocyclitol-aminoglycosides such as 1,3-di-de-N-amidinodihydrostreptomycin. Tylosin, U.S. Pat. No. 3,178,341, Merck Index 9th Ed., No. 9486 is sold commercially as a veterinary antibiotic; spiromycin is disclosed in U.S. Pat. No. 2,943,023, Merck Index 9th Ed., No. 8525; leucomycin is disclosed in Merck Index 9th., No. 5307; magnamycin is disclosed in U.S. Pat. No. 2,960,438 and Merck Index 9th Ed., No. 1812 and oleandomycin is disclosed in U.S. Pat. Nos. 2,757,123 and 2,842,481 and Merck Index 9th Ed., No. 6671.
A nucleoside is a combination of a sugar, either ribose (in RNA) or 2′-deoxyribose (in DNA), with a purine or pyrimidine base. Examples of a nucleoside include but are not limited to adenosine, cytidine, guanosine, uridine, 2′-deoxyadenosine, 2′-deoxyguanosine, 2′-deoxycytidine, 2′-deoxythymidine, and the like.
A derivative of a carbohydrate compound is presented in accordance with the present invention. The carbohydrate compound is selected from a sugar, an amino sugar, a sugar alcohol, an amino glycoside, a deoxysugar, a glycoside, a nucleoside, a substituted sugar, a substituted amino sugar, a substituted deoxysugar, a substituted sugar alcohol, a substituted glycoside, a substituted aminoglycoside, a substituted nucleoside, an aminocyclitol, an aminoglycoside-aminocyclitol, and the like in an embodiment of the present invention.
The derivative further comprises a group of formula I:




wherein the group is in place of at least one hydrogen atom of at least one hydroxyl group of the aforementioned carbohydrate compounds, or, when present, of at least one amino group of the aforementioned carbohydrate compounds. The substituent R1 is selected from an alkyl group or an azaalkyl group, and R2 is selected from a primary or secondary amino group.

In an embodiment of the present invention, derivatives of the carbohydrate glucosamine having two groups of formula I are presented wherein R1 is —(CH2)3NH(C H2)4NH(CH2)3—, R2 is —NH2, and R3 is OH (α and β anomers) (4a); R1 is —(CH2)3NH(CH2)4NH(CH2)3—, R2 is —NH2, and R3 is α-OCH3 (4b); R1 is —(CH2)3NH(CH2)4NH(CH2)3—, R2 is —NH2, and R3 is α-OCH2Ph (4c);




R1 is —(CH2)3NH(CH2)4NH(CH2)3—, R2 is —NH2, and R3 is β-OCH2Ph (4d); and R1 is —(CH2)3NH(CH2)4NH(CH2)3—, R2 is —NH2, and R3 is  ̃OH (4e).
In a second embodiment of the present invention, derivatives of the carbohydrate 2′-deoxyadenosine having the group of formula I are presented wherein R1 is —CH2CH2CH2NH(CH2)4NH(CH)3— and R2 is —NH2 (7); R1 is —CH2CH2CH2NH(CH2)4NH(CH)3— and R2 is —NH2 (9); and R1 is —CH2CH2CH2NH(CH2)4NH(CH)3— and R2 is —NH2 (11).




In a third embodiment of the present invention, derivatives of the carbohydrate neomycin having the group of formula I are presented wherein R1 is —CH2CH2— and R2 is —NH2 (14a), and R1 is —CH2CH2NHCH2CH2— and R2 is —NH2 (14b).




In a fourth embodiment of the present invention, derivatives of the carbohydrate neamine having the group of formula I are presented wherein R1 is —CH2CH2— and R2 is —NH2 (17a), and R1 is —CH2CH2CH2NH(CH2)4NH(CH2)3— and R2 is —NH2 (17b)




In a fifth embodiment of the present invention, derivatives of the carbohydrate Me-neobiamine having a group of formula I are presented wherein R1 is —CH2CH2 NH(CH2)2— and R2 is —NH2 (20a), and R1 is —CH2CH2CH2 NH(CH2)4NH(CH2)3— and R2 is —NH2 (20b).




In a sixth embodiment of the present invention, derivatives of the carbohydrate kanamycin having the group of formula I are presented wherein R1 is —CH2CH2—, R2 is —NH2, and R3 is OH (23a); R1 is —CH2CH2NHCH2CH2—, R2 is NH2, and R3 is OH (23b); R1 is —CH2CH2CH2NH(CH2)4NH(CH2)3—, R2 is —NH2, and R3 is —OH (23c); and R1 is —CH2CH2—, R2 is —NH2, and R3 is NH2 (24). The kanamycin derivative (25) is also presented.




EXPERIMENTAL
The following are examples of the preparation of the aforementioned compounds in accordance with the present invention.
Materials
Candida antarctica lipase B (CAL-B, Novozyme 435) was obtained from Novozymes North America, (Franklinton, N.C., USA) as a gift. Pseudomonas fluorescence lipase (PFL) was purchased from Amano (Nagoya, Japan). Fast Flow Sepharose SP (FF Sepharose SP), High Performance SP Sepharose (HP Sepharose SP) and Source 15S stationary phase materials were donated by Amersham Pharmacia (Uppsala, Sweden). (note: while the Sepharose materials are agarose based, the Source resins consist of hydrophilized polystyrene divinylbenzene).
The compounds 2′-deoxyadenosine, glucosamine, mannosamine, kanamycin A & B, neomycin sulfate, spermine, calf thymus DNA, chicken egg lysozyme, horse heart cytochrome-C, ammonium bicarbonate, sodium phosphate (dibasic), and sodium phosphate (monobasic) were purchased from Sigma (Saint Louis, Mo.). Ethylenediamine, diethylenetriamine, vinyl chloroformate and dry THF were purchased from Aldrich (Milwaukee Wis.). Acetone-O-(vinyloxy)carbonyl)oxime was prepared according to literature protocol, Garcia-Alles, L. F.; Magdalena, J.; Gotor, V.; J. Org. Chem. 1996, 61, 6980-6986, which is incorporated by reference herein.
The glucosamine analogs (compounds 1b-1e) neamine (compound 5) and methyl neobiosamine (compound 8) were prepared according to literature procedures: Shafizadeh, F.; Meshreki, M. H.; R. A. Susott; J. Org. Chem. 1973, 38, 1190-1194; Gross, P. H., Jeanloz, R. W., J. Org. Chem. 1967, 32, 2759-2763; and Rinehart, K. L., Argoudelis, A. D.; Goss, W. A., Sohler, A., Schaffner, C. P. J. Am. Chem. Soc. 1996, 82, 3938-3946, all of which are incorporated by reference herein.
1H and 13C NMR spectra were recorded on a Varian spectrometer with TMS as the internal standard. Chemical shifts are reported in ppm and the coupling constants (J) are given in Hertz (Hz). ESI-MS and MALDI-TOF were measured on a Varian mass spectrometer. Flash chromatography was performed on 60-200 mesh silica gel (Sigma MO). Product yields, purities and spectroscopic data is provided in the supporting information section. Cation-exchange chromatography was performed on Fast Flow Sepharose SP (FF Sepharose SP) using ammonium bicarbonate (NH4HCO3) as a mobile phase. Fluorescence and absorbance analyses were carried out using a Perkin Elmer plate reader and the results were analyzed using the software HTSoft 2.0.
Procedures
I. Generation of Glucosamine and Mannosamine Derivatives.
Scheme 1 depicts a chemoenzymatic synthesis of glucosamine-based and mannosamine-based derivatives in accordance with the present invention. Referring to Scheme 1, the synthesis of vinyl carbamate linkers, 2a-2e, is presented in an embodiment of the present invention. Vinyl chloroformate (426 μl, 5.0 mmol) was added drop-wise to a phosphate buffer solution (40 ml, pH 8.0, 50 mM) of compounds (1a-1e) (2.0 mmol) for 1 h at 0° C. The reaction mixture was vigorously stirred and the solution was maintained at pH 8.0 by continuously adding 1.0 N NaOH. After 5 h, compounds 2c and 2d were directly precipitated from the buffer solution and then washed by distilled H2O and dried under vacuum with >95% purity. For the other compounds, the reaction mixture was lyophilized for 24 h to afford crude product, which was purified by silica gel flash chromatography using EtOAc/MeOH (5:1 and 2:1). The above procedure resulted in moderate to good yields of 2a, 88%; 2b, 33%; 2c, 42%; 2d, 67%, 2e, 80%.
Lipase-catalyzed regioselective synthesis of 6-vinylcarbonate linkers, 3a-3e, is presented in an embodiment of the present invention. Compounds 2a-2e (0.6 mmol), acetone O-(vinyloxy)carbonyl)oxime (1.8 mmol), and Candida antarctica lipase B (CAL) in 15 ml of dry THF were shaken at 200 rpm at 45° C. for 24-96 hr. The reaction was monitored by TLC. After evaporation of the solvent, the residue was purified by flash chromatography using hexane/EtOAc (2:1, 1:2) to afford 3a-3e. The yields were 3a, 91%; 3b, 73%; 3c, 83%; 3d, 48%; 3e, 82%. The 6-vinyloxy derivatives were the sole products in most cases.
Generation of spermine derivatives of glucosamine and mannosamine, 4a-4e, is presented in an embodiment of the present invention. A solution of the vinyloxy linkers, 3a-3e, (0.2 ̃0.4 mmol) and spermine (3 equiv relative to free amine group) in ethanol (10 ml) was shaken at 45° C. and 250 rpm for 96 h. After removal of ethanol under pressure, the residue was neutralized with 1.0 N HCl at 0° C. After lyophilization the powder was purified using cation-exchange chromatography (resin: FF Sepharose SP, eluent: 0.1-0.5 M NH4HCO3 solution) as described infra. The fraction collection was monitored by TLC and detected by ninhydrin reagent solution after heating at 100° C.
The NH4HCO3 solution was removed by lyophilization to yield the desired products (4a-4e) with purities ranging from 85 ̃95% based on NMR and MS analyses and isolated yields ranging from 10% ̃25% after cation-exchange chromatography. It was observed that the formation of isomers was usually lower than 20 ̃40%, presumably due to stronger steric effects of secondary amino than the primary amino groups in spermine. The mannosamine-spermine derivative (4e) was synthesized in a similar manner with a 23% overall yield.




II. Generation of 2′-deoxyadenosine Derivatives

Scheme 2 depicts a chemoenzymatic synthesis of a 2′-deoxyadenosine derivative containing a spermine chain at the 6′-hydroxyl group and a 2′-deoxyadenosine derivative containing a spermine on the 3′-hydroxyl group in accordance with the present invention. Referring to scheme 2, the synthesis of monospermine derivatives of 2′-deoxyadenosine, 7 and 9, is presented in an embodiment of the present invention.
The vinyl linker 6, was readily formed using CAL-B catalyzed acylation with high yields (87%) per liter according to literature protocol, Rinehart, K. L.; Argoudelis, A. D.; goss, W. A.; Sohler, A.; Schaffner, C. P. J. Am. Chem. Soc. 1996, 82, 3938-3946 which is incorporated by reference herein. Aminolysis with excess spermine gave the desired product, 7. A solution of the vinyloxy derivative 6 (0.3 mmol) and spermine (0.9 mmol) in THF (20 ml) was shaken at 30° C. and 250 rpm for 24 h. After removal of THF the residue was purified by silica gel flash chromatography using MeOH/1.0 M NaCl (10:1) to yield the pure product 7 (69% yield after flash chromatography).
Pseudomonas fluorescence lipase (PFL) was used to catalyze the acylation of 2′-deoxyadenosine. The vinyl carbonate linker was introduced at 3′-hydroxyl as described above, with high regioselectivity (>10:1, 3′-OH versus 6′-OH group) to yield the intermediate product, 8 in reasonable yield (28%) according to literature protocol, Rinehart, K. L.; Argoudelis, A. D.; goss, W. A.; Sohler, A.; Schaffner, C. P. J. Am. Chem. Soc. 1996, 82, 3938-3946 which is incorporated by reference herein. The desired monospermine derivative, 9 was obtained upon aminolysis with spermine (50% yield, 95% purity).







Scheme 3 depicts a chemoenzymatic synthesis of a 2′-deoxyadenosine derivative having multiple spermine chains in accordance with the present invention. Referring to scheme 3, the synthesis of a polyspermine derivative of 2′-deoxyadenosine, 11, is presented in an embodiment of the present invention. Vinyl chloroformate (307□1, 5.4 mmol) was added drop-wise to 5 (377 mg, 1.5 mmol) in pyridine (5 ml) and DMAP (122 mg, 1.0 mmol) at 0° C. The reaction mixture was stirred at room temperature for 24 h after which the reaction mixture was diluted with EtOAc (20 ml) and the mixture was washed with 1.0 N HCl, saturated NaHCO3, followed by saturated NaCl.




The organic phase was dried over MgSO4. After evaporation of solvent the residue was purified by flash chromatography (hexane/EtOAc, 1:1 and 1:5) to afford the product 10 (yield, 28%). The polypermine derivative, 11 (yield 32%, purity, 85%), was synthesized in a manner similar to that described in the procedure above for the generation of spermine derivatives of glucosamine and mannosamine, 4a-4e.
III. Generation of Polyamine Derivatives of Neomycin, Neamine, and Methyl-Neobiosamine
Scheme 4 depicts a synthesis of derivatives of neomycin 12, neamine 15, and methyl-neobiosamine 18 in accordance with the present invention. Referring to Scheme 4, the synthesis of a spermine derivative of neomycin is presented in an embodiment of the present invention. The vinyl carbamate linkers of neomycin, neamine and methyl-neobiosamine (13, 16, 19) were synthesized as described for the synthesis of the vinyl carbamate linkers 2a-2e in moderate to good yields (13, 71%; 16, 66%; 19, 48%, respectively).
A solution of vinyloxy linkers 13 and 16, (0.2 ̃0.4 mmol) and ethylenediamine (2 ml) were shaken at 35° C. and 250 rpm for 24-48 h. The excess ethylenediamine was evaporated under pressure and the residue was precipitated by MeOH/EtOAC and then washed with EtOAc to yield pure products: 14a and 17a respectively.
A solution of vinyloxy linkers 13 and 19 (0.3 mmol) and diethylenetriamine (4 equiv relative to free amine group) in ethanol (10 ml) was shaken at 45° C. and 250 rpm for 96 h. After removal of ethanol under vacuum, the residue was precipitated and washed as described in procedure 4 to afford 14b and 20a respectively.
The spermine derivatives of neamine and methyl-neobiosamine, 17b and 20b, respectively were synthesized according to the procedure for the generation of spermine derivatives of glucosamine and mannosamine above and were obtained in moderate to good yields.










IV. Generation of Polyamine Derivatives of Kanamycin

Scheme 5 depicts a generation of polyamine derivatives of kanamycin in accordance with the present invention. Referring to scheme 5, the synthesis of vinyl carbamate linkers (22a and 22b) is presented in an embodiment of the present invention. The carbamate linkers for kanamycin A and B were synthesized according to the procedure for the generation of spermine derivatives of glucosamine and mannosamine above and were obtained in moderate to good yields; 22a, yield 37%, 22b, yield 84%.
The derivatives 22a or 22b (0.2 ̃0.4 mmol), and ethylenediamine (2 ml) were shaken at 35° C. and 250 rpm for 24-48 h. The excess ethylenediamine was evaporated under pressure and the residue was precipitated by MeOH/EtOAC and then washed with EtOAc to yield pure products 23a and 24, respectively.
A solution of 22a (0.3 mmol) and diethylenetriamine (4 equiv relative to free amine group) in ethanol (10 ml) was shaken at 45° C. and 250 rpm for 96 h. After removal of ethanol in vacuo the residue was precipitated and washed as procedure A to afford 23b (yield, 76%).
The spermine derivatives 23c and 25 (structure deduction based on ESI-MS, 1H and 13C NMR data), were synthesized according to the procedure for the generation of spermine derivatives of glucosamine and mannosamine above and were obtained in moderate to good yields (7% and 27% respectively) with purities >95% after cation exchange chromatography.




A method for separating one or more components of a biomolecule mixture is presented in accordance with the present invention. The means of separation is an ion exchange chromatographic system operated in a displacement mode. The displacement mode comprises sequentially perfusing the chromatographic system with a first solution comprising the biomolecule mixture and a second solution comprising a derivative of a carbohydrate compound.
The derivative of the carbohydrate compound is chosen from any of the aforementioned carbohydrate derivatives described supra in an embodiment of the present invention. The biomolecule mixture may include but is not limited to mixtures of proteins, including gylcosylated proteins, peptides, nucleotides, nucleosides, oligonucleotides, sphingolipids, phospholipids, and the like.
A modified batch displacement assay was used to investigate displacer efficacy of the carbohydrate derivatives over a wide range of concentrations. The carbohydrate derivatives from hereon will be referred to as the displacer candidates unless otherwise specified. Different input concentrations of the displacer candidates were employed to determine the DC50 value, which is the input displacer concentration required to displace fifty percent of the initially bound protein. The lower the DC50 value the more efficacious is the displacer candidate.
FIG. 1 depicts a graph for the displacement of cytochrome-C by various input concentrations of neamine and its derivatives on HP Sepharose SP in accordance with the present invention. Referring to FIG. 1, the Y axis is % cytochrome-C displaced and the X axis is input displacer concentration in mmol. The curves 103, 104, and 105 are neamine, 17a, and 17b respectively. The resulting plots were then employed to determine the DC50 values of neamine (DC50, 5.6 mM), 17a (DC50, 2.1 mM) and 17b (DC50, 0.7 mM).
Table 1 is of displacer candidates and their respective DC50 values of horse cytochrome-C on HP Sepharose SP and Source 15S cation exchange resins in accordance with the present invention. Column 201 is the displacer candidate evaluated. Column 202 is DC50 values of horse cytochrome-C on HP Sepharose SP. Column 203 is the DC50 values of horse cytochrome-C on Source 15S cation exchange resin. The above approach was employed to determine the DC50 values of the displacer candidates for the displacement of horse cytochrome-C on HP Sepharose SP and Source 15S cation exchange resins at pH 6.0.









TABLE 1






DC50-Cytochrome C
DC50-Cytochrome C


Displacer
on HP Sepharose SP (mM)
on Source 15S (mM)







17b
0.7 ± na 
0.6 ± 0.03


23c
1.0 ± na 
0.9 ± 0.08


25
1.0 ± 0.02
2.4 ± 0.13


14b
1.1 ± 0.06
0.9 ± 0.12


20b
1.1 ± na 
0.8 ± 0.04


 4c
1.3 ± 0.08
0.8 ± 0.02


14a
1.6 ± 0.01
1.3 ± 0.09


24
1.9 ± 0.01
1.9 ± 0.06


23a
2.0 ± 0.15
1.7 ± 0.02


17a
2.1 ± 0.06
2.3 ± 0.04


11
2.3 ± na 
1.1 ± 0.14


 4e
2.7 ± 0.68
1.1 ± 0.00


 4a
2.8 ± na 
0.9 ± 0.07


 4d
2.8 ± 0.20
0.8 ± 0.00


Neomycin
2.8 ± 0.87
1.7 ± 0.02


 4b
3.6 ± 0.25
0.8 ± 0.04


23b
4.1 ± 0.29
2.4 ± 0.13


Spermine
4.8 ± 1.04
4.3 ± 0.64


Neamine
5.6 ± 1.99
4.9 ± 1.67


Bekanamycin
6.2 ± 0.37
3.1 ± 2.29


Spermidine
7.7 ± 1.44
5.8 ± 0.44


20a
9.4 ± 2.65
4.8 ± 0.03


Diethylenetriamine
10.8 ± 0.19 
14.4 ± 3.67 


 7
11.7 ± 0.10 
6.2 ± 0.46


 9
12.3 ± 0.25 
12.9 ± 1.46 


Ethylenediamine
20.2 ± 2.67 
17.6 ± 2.15 









Referring to Table 1, while commercially available displacers such as spermine and neomycin show moderate to high affinities as displacers with DC50 values of 4.8 and 2.8 mM, respectively; compounds 17b (neamine tetraspermine) and 23c (kanamycin A tetraspermine) showed sub-millimolar DC50 values. Furthermore, eleven displacers exhibited higher affinities than neomycin while the others had comparable affinities. These results are important in that they demonstrate that individual displacers with moderate affinities can be conjugated to generate a new class of high affinity displacers. This represents a novel approach for the design of high affinity displacers for biomolecule purification by displacement chromatography.
The DC50 values of neomycin and its derivatives 14a (neomycin derivatized with ethylenediamine) and 14b (neomycin derivatized with diethylenetriamine) were 2.8, 1.6 and 1.1 mM, respectively for the displacement on HP Sepharose SP. This indicates that displacer affinity increases as larger polyamine homologues are conjugated to neomycin. Neomycin derivatized with diethylenetriamine 14a was found to have the highest affinity among the neomycin derivatives. It turns out that the displacer affinity for the molecules as well as their derivatives followed the trend neomycin>neamine>neobiosamine.
Glucosamine and mannosamine derivatives 4a-4e showed interesting trends in their DC50 values on HP Sepharose SP. The DC50 values of 4a, 4d and 4e are similar ( ̃2.7-2.8 mM). However, 4c and 4b show very different affinities. While 4c (DC50=1.3 mM) has the highest affinity among this family of compounds, 4b (DC50=3.6 mM) has the lowest affinity.
The influence of the stationary phase on displacer affinity was investigated using a second strong cation exchange resin, Source 15S. The performance of the displacer candidates on Source 15S is significantly different from that observed on HP Sepharose SP, with as many as eight displacers exhibiting sub-millimolar affinities. Although neamine-tetraspermine (17b) and kanamycin A-tetraspermine (23c) were still among the highest affinity displacers with DC50 values of 0.6 and 0.9 mM, respectively; other displacers including 4b, 4c, 4d, 4a, 14b and 20b had comparable sub-millimolar affinities.
The affinities of the glucosamine/mannosamine derivatives (4a-4e) on the Source 15S resin showed significant differences when compared to their affinities on HP Sepharose SP. The DC50 values of these molecules ranged between 0.8 to 1.1 mM for the Source resin indicating that these were among the highest affinity molecules on that resin. The glucosamine/mannosamine-derivatives (4a-4e) follow the affinity trend 4b-4c-4d>4a>4e (DC50 values: 0.8, 0.8, 0.8, 0.9 and 1.1 mM respectively). It is also interesting to note that 4b (DC50, 3.6 mM), the least effective displacer among this family of molecules on the HP Sepharose SP resin, was the most effective on the Source resin (DC50, 0.8 mM). The trend described above indicates that displacer efficacy on the Source resin increased with the introduction of hydrophobic/aromatic moieties in the molecule. These results indicate that although the displacer candidates were designed for generic high affinity displacers, unique selectivities can be observed on different resins.
FIG. 2 depicts a graph comparing the % lysozyme and % cytochrome-C displaced on HP Sepharose SP in accordance with the present invention. The Y axis is % protein displaced. The X axi is the displacer candidate evaluated. The displacer candidate concentration is 2.5 mM in an embodiment of the present invention. In order to evaluate the displacer candidates with another protein, experiments were carried out with chicken-egg lysozyme adsorbed on HP Sepharose SP.
Referring to FIG. 2, a comparison of the percent protein displaced for both lysozyme and cytochrome-C at displacer concentrations of 2.5 mM is shown. The data is arranged in increasing order of percent lysozyme displaced. A large number of the displacer candidates had significantly higher affinities than those of the previously identified commercial compounds neomycin and spermine. In addition, molecules such as kanamycin A tetraspermine (23b) and neamine tetraspermine (17b) were found to be particularly effective at displacing lysozyme with values of 67.8 and 52.8 percent protein displaced, respectively.
As seen from these screening results, the rational design of displacer candidates has resulted in the identification of several novel high affinity displacers for cation exchange systems. These molecules have the potential to significantly improve the efficiency of ion exchange processes ranging from large scale preparative chromatography to microscale proteomic applications.
Experimental
The following is an example of the procedure for separating one or more components of a biomolecule mixture by the means of an ion exchange chromatographic system in accordance with the present invention.
Purification of the Aminoglycoside-Polymamine Displacer Candidates
The aminoglycoside-polyamine compounds were purified prior to use as follows. In the case of ethylenediamine, the desired aminoglycoside polyamines were produced in a high yield and good purity after the evaporation of excess ethylenediamine in vacuo and simple precipitation with a mixture of ethyl acetate and methanol (for example, 14a and 17a, >99% yield, >95% purity).
For the purification of diethylenetriamine and spermine derivatives, a parallel batch screen using resin packed in a membrane-bottomed 96-well microtiter plate was used to identify the right resin-mobile phase combination for the subsequent chromatography steps. Cation-exchange chromatography using Fast Flow Sulfopropyl Sepharose (FF Sepharose SP) with a multi-step gradient of ammonium bicarbonate were identified as the best candidates for the stationary phase and the mobile phase conditions respectively (screening data not shown). The fact that ammonium bicarbonate could be removed from the final product by freeze-drying was also a significant factor in its selection as the mobile phase.
Protein Adsorption
The bulk stationary phase (HP Sepharose SP or Source 15S) was first washed once with de-ionized water and then three times with the buffer, (50 mM phosphate, pH 6.0) and allowed to equilibrate for 2 hours. After gravity-settling of the stationary phase, the supernatant was removed and 3.0 mL of the remaining stationary phase slurry was equilibrated with 36 ml containing 3 mg/ml of the protein (horse heart cytochrome-C or chicken egg lysozyme) in 50 mM phosphate buffer, pH 6.0, at 20° C.
The protein was equilibrated with the resin for five hours in order to attain complete equilibration during which, the stationary phase was allowed to gravity-settle. Upon settling, the supernatant was removed and the protein content in the supernatant was determined using absorbance detection at 280 or 405 nm using a plate reader. The mass of the protein adsorbed on the stationary phase was determined by mass balance.
Determination of DC50 
For the screening experiments, 300 μL of different initial concentrations (ranging from 0.3 to 5 mM) of a displacer solution was added to 25 μL aliquots of the stationary phase slurry with bound protein. (note: a different displacer candidate and concentration were employed for each vial to enable parallel screening). The system was equilibrated for 5 h. After equilibrium was achieved, the supernatant was removed and the protein content was determined by absorbance detection at 280 or 405 nm using a plate reader.
The percent protein displaced, was calculated for each aliquot based on the protein mass balance and the data was plotted as a function of the initial displacer concentration. The resulting plots were then employed to determine the initial displacer concentration required to displace fifty percent of the adsorbed protein (i.e. the DC50).
A method for condensing DNA comprising combining the DNA with at least one of the aforementioned derivatives of a carbohydrate compound wherein the DNA is bound to the carbohydrate compound is presented in accordance with the present invention. FIG. 3 depicts a graph of DNA binding efficacy of the displacer candidates in an embodiment of the present invention. The Y axis is % fluorescence decreased and the X axis is the carbohydrate derivative evaluated.
Referring to FIG. 3, an ethidium bromide displacement assay was employed to evaluate the DNA-binding affinity of carbohydrate derivatives in a 96-well format. Using this screen, the percent fluorescence decreased was used as a parameter to rank the DNA-binding efficacy of the various compounds.
Commercially available polyamines such as spermidine, spermine, bekanamycin and neomycin showed relatively low efficacies. On the other hand, a large number of the carbohydrate derivatives acted as effective DNA binding agents. Particularly significant are the results with 23c (kanamycin A-tetraspermine), 4a, 25 and 4b, all of which resulted in greater than 60% fluorescence decreased. This data demonstrates that the aminoglycoside polyamine displacers exhibit high DNA-binding efficacies.

## Claims

1. A derivative of a carbohydrate compound ,said derivative selected from

2. A method for separating one or more components of a biomolecule mixture by means of an ion exchange chromatographic system operated in the displacement mode, said method comprising: sequentially perfusing the system with a first solution comprising the biomolecule mixture, and a second solution comprising a derivative of a carbohydrate compound according to claim 1.

3. A method for separating a protein or peptide mixture by means of an ion exchange chromatographic system operated in the displacement mode, said method comprising: sequentially perfusing the system with a first solution comprising said mixture, and a second solution comprising a derivative of a carbohydrate compound according to claim 1.

4. The method according to claim 1, wherein the concentration of the derivative of a carbohydrate compound in the second solution is less than 5 mM.

5. A method for condensing DNA, said method comprising:
combining DNA with at least one derivative of a carbohydrate compound according to claim 1, wherein the DNA is bound to the derivative of the carbohydrate compound.