WO2001010890A2 - Process of synthesis of fluorescent protease substrates - Google Patents

Process of synthesis of fluorescent protease substrates Download PDF

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Publication number
WO2001010890A2
WO2001010890A2 PCT/US2000/021710 US0021710W WO0110890A2 WO 2001010890 A2 WO2001010890 A2 WO 2001010890A2 US 0021710 W US0021710 W US 0021710W WO 0110890 A2 WO0110890 A2 WO 0110890A2
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Prior art keywords
formula
compound
ylamino
oxo
chromen
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PCT/US2000/021710
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French (fr)
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WO2001010890A3 (en
Inventor
Nathan Collins
Luke J. Gosink
James E. Ii Sheppeck
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Chemrx Advanced Technologies, Inc.
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Priority to AU65323/00A priority Critical patent/AU6532300A/en
Publication of WO2001010890A2 publication Critical patent/WO2001010890A2/en
Publication of WO2001010890A3 publication Critical patent/WO2001010890A3/en

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    • C—CHEMISTRY; METALLURGY
    • C40—COMBINATORIAL TECHNOLOGY
    • C40B—COMBINATORIAL CHEMISTRY; LIBRARIES, e.g. CHEMICAL LIBRARIES
    • C40B50/00—Methods of creating libraries, e.g. combinatorial synthesis
    • C40B50/14—Solid phase synthesis, i.e. wherein one or more library building blocks are bound to a solid support during library creation; Particular methods of cleavage from the solid support
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K1/00—General methods for the preparation of peptides, i.e. processes for the organic chemical preparation of peptides or proteins of any length
    • C07K1/04—General methods for the preparation of peptides, i.e. processes for the organic chemical preparation of peptides or proteins of any length on carriers
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K1/00—General methods for the preparation of peptides, i.e. processes for the organic chemical preparation of peptides or proteins of any length
    • C07K1/04—General methods for the preparation of peptides, i.e. processes for the organic chemical preparation of peptides or proteins of any length on carriers
    • C07K1/047—Simultaneous synthesis of different peptide species; Peptide libraries
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K5/00—Peptides containing up to four amino acids in a fully defined sequence; Derivatives thereof
    • C07K5/04—Peptides containing up to four amino acids in a fully defined sequence; Derivatives thereof containing only normal peptide links
    • C07K5/08—Tripeptides
    • C07K5/0815—Tripeptides with the first amino acid being basic
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07B—GENERAL METHODS OF ORGANIC CHEMISTRY; APPARATUS THEREFOR
    • C07B2200/00—Indexing scheme relating to specific properties of organic compounds
    • C07B2200/11—Compounds covalently bound to a solid support

Definitions

  • the present invention relates to synthesis of protease substrates.
  • protease substrates typically are peptide(s) or peptide derivative(s) covalently bound to a fluorescent moiety precursor (L) or an array of the same.
  • protease substrates i.e., peptides or peptide derivatives covalently bound to a fluorescent moiety through an amide or an ester bond.
  • Enzymes including proteases, having affinity for peptides or peptide derivatives cleave the bond between the peptide or peptide derivative and the fluorescent moiety, thereby releasing the fluorescent moiety.
  • Spectroscopic detection/measurement of the release of the fluorescent moiety is then used to determine the structural characteristics of the binding peptide and also the level of such a binding to a given enzyme.
  • the present invention provides a process for synthesizing a compound or an array of compounds of Formula I and Formula-6 wherein peptidal substrates are bound to a solid support and a fluorescent moiety. Also provided is a process for synthesizing for synthesizing compounds of Formula II wherein peptidal substrates are bound to a fluorescent moiety. These related processes afford said peptidal substrates having a varied structural order.
  • the present invention also provides novel compounds of Formula-3 which are useful in the processes of the present invention.
  • the present invention provides a process for synthesizing a compound or an array of compounds of Formula I:
  • R 1 represents a protected or unprotected natural or unnatural amino acid side chain
  • R 2 represents a protected or unprotected natural or unnatural amino acid side chain
  • R 3 represents H or C 1 4 -alkyl
  • R 2 and R 3 along with the carbon and nitrogen atom to which they are attached form a five to ten membered hetero cyclic ring;
  • R 4 represents R 4a or H;
  • R 4a represents R 5 , SO 2 -R !0 , CO-OR 10 , C(O)-NH-R 10 , C(S)-NH-R 10 , C(O)-R 10 or C(S)-
  • L represents a fluorescent moiety
  • SS represents a solid support
  • R 5 represents an amino acid protecting group
  • R 10 represents H, aryl, (CH 2 ) 1 6 aryl, (CH,) 0.6 heteroaryl, C,_ 8 alkyl, C 4 14 branched alkyl or C ⁇ cycloalkyl; the process comprising the steps of
  • Preferred embodiments of the present invention provide a process wherein L represents a fluorescent moiety selected from 4-methyl-2-oxo-2H-chromen-7- ylamino, 2-oxo-4-trifluoromethyl-2H-chromen-7-ylamino, 4- methoxycarbonylmethyl-2-oxo-2H-chromen-7-ylamino, 2-oxo-4-(2-oxo-ethyl)-2H- chromen-7-ylamino, 2-oxo-2H-chromen-7-ylamino, 4-nitro-phenylamino, 5- dimethylsulfamoyl-naphthalen-1 -ylamino, naphthalen-1 -ylamino, 5-methoxy- naphthalen-1 -ylamino, and rhodamino; and SS represents a solid support selected from PALS.
  • L represents a fluorescent moiety selected from 4-methyl-2-oxo-2H-chromen-7- ylamino, 2-o
  • step (i)(a) is selected from NaBH(OAc) 3 , diborane, BH 3 .pyridine, BH 3 .dimethylsulfide, BH 3 .THF, NaBH 4 , NaCNBH 3 , Zn(BH 4 ) 2 and LiBH 4 .
  • a further preferred embodiment provides a process wherein L represents 4-methyl-2-oxo-2H-chromen-6-ylamino.
  • Another aspect of the present invention provides a process for synthesizing a compound or an array of compounds of Formula II
  • R represents a protected or unprotected natural or unnatural amino acid side chain
  • R 2 independently at each occurance represents a protected or unprotected natural or unnatural amino acid side chain
  • R 3 independently at each occurance represents H or C -alkyl; alternatively R 2 and R 3 independently at each occurance along with the carbon and nitrogen atom to which they are attached form a five to ten membered hetero cyclic ring;
  • R 4 represents R 4a or H
  • R 4a represents R 5 , SO 2 -R 10 , CO-OR 10 , C(O)-NH-R 10 , C(S)-NH-R 10 , C(O)-R 10 or C(S)-
  • R 10 represents a fluorescent moiety
  • R 5 represents an amino acid protecting group
  • R 10 represents H, aryl, (CH,) 1 6 aryl, (CH ⁇ heteroaryl, C, .g alkyl, C 4 14 branched alkyl or C ⁇ cycloalkyl;
  • n represents an integer from 1 to 7; said process comprising
  • R 1 , R 2 , R 3 , R 4 ⁇ SS, "n" and L are as defined above;
  • R 1 , R 2 , R 3 , SS, "n" and L are as defined above;
  • Yet another related process of the present invention provides a process for synthesizing a compound or an array of compounds of Formula II
  • R 1 represents a protected or unprotected natural or unnatural amino acid side chain
  • R 2 independently at each occurance represents a protected or unprotected natural or unnatural amino acid side chain
  • R 3 independently at each occurance represents H or C,_ 4 -alkyl
  • R 2 and R 3 independently at each occurance along with the carbon and nitrogen atom to which they are attached form a five to ten membered hetero cyclic ring;
  • R 4 represents R 4a or H;
  • R 4a represents R 5 , SO 2 -R 10 , CO-OR 10 , C(O)-NH-R 10 , C(S)-NH-R 10 , C(O)-R 10 or C(S)-
  • L represents a fluorescent moiety
  • R 5 represents an amino acid protecting group
  • R 10 represents H, aryl, (CH,), . , ; aryl, (CH,) ⁇ heteroaryl, C 1 8 alkyl, C 4.14 branched alkyl or ,_ 14 cycloalkyl; and
  • n represents an integer from 1 to 7; said process comprising
  • R 1 , R 2 , R 3 , SS, "n" and L are as defined above;
  • R 4a is as defined above, to form a compound of Formula-6;
  • L represents a fluorescent moiety selected from 4- methyl-2-oxo-2H-chromen-7-ylamino, 2-oxo-4-trifluoromethyl-2H-chromen-7- ylamino, 4-methoxycarbonylmethyl-2-oxo-2H-chromen-7-ylamino, 2-oxo-4-(2- oxo-ethyl)-2H-chromen-7-ylamino, 2-oxo-2H-chromen-7-ylamino, 4-nitro- phenylamino, 5-dimethylsulfamoyl-naphthalen-l -ylamino, naphthalen-1 -ylamino, 5-methoxy-naphthalen-l -ylamino, and rhodamino; and SS represents a solid support selected from PALS.
  • L represents 4- methyl-2-oxo-2H-chromen-7-ylamino, 2-oxo-4-trifluoromethyl-2H-chromen-7-
  • R 1 represents a protected or unprotected natural or unnatural amino acid side chain
  • R 2 independently at each occurance represent a protected or unprotected natural or unnatural amino acid side chain
  • R 3 independently at each occurance represents H or C 1 4 -alkyl
  • R 2 and R 3 independently at each occurance along with the carbon and nitrogen atom to which they are attached form a five to ten membered hetero cyclic ring;
  • R 4 represents R 4a or H
  • R 4a represents R 5 , SO 2 -R 10 , CO-OR 10 , C(O)-NH-R 10 , C(S)-NH-R 10 , C(O)-R 10 or C(S)-
  • L represents a fluorescent moiety
  • SS represents a solid support
  • R 5 represents an amino acid protecting group
  • R 10 represents H, aryl, (CH, ⁇ heteroaryl, (CH j ), ⁇ aryl, C 1 8 alkyl, C 4 14 branched alkyl, or ⁇ cycloalkyl;
  • n represents an integer from 1 to 7; the process comprising treating a compound of Formula A
  • Another aspect of the present invention provides a compound of Formula-3
  • R 1 represents a protected or unprotected natural or unnatural amino acid side chain
  • L represents a fluorescent moiety
  • SS represents a solid support.
  • Preferred compounds of Formula-3 are those wherein L represents a fluorescent moiety selected from 4-methyl-2-oxo-2H-chromen-7-ylamino, 2-oxo-4- trifluoromethyl-2H-chromen-7-ylamino, 4-methoxycarbonylmethyl-2-oxo-2H- chromen-7-ylamino, 2-oxo-4-(2-oxo-ethyl)-2H-chromen-7-ylamino, 2-oxo-2H- chromen-7-ylamino, 4-nitro-phenylamino, 5-dimethylsulfamoyl-naphthalen-l- ylamino, naphthalen-1 -ylamino, 5-methoxy-naphthalen-l -ylamino, and rhodamino.
  • Synthesis of compounds of Formula-3 can be accomplished by the procedure of Boojamra, C. G.; Burow, K. M.; Thompson, L. A.; Ellman, J. A. J. Org. Chem. 1997, 62, 1240-1256. A general procedure is discussed below.
  • a suspension/mixture of an acid salt of a compound of Formula-1 (1.5 eq. wit to a compound of Formula- 2A) and a 2 % AcOH solution in DMA is combined with a reducing agent, e.g., sodium triacetoxyborohydride [NaHB(OAc) 3 , 1.5 to 3 eq.].
  • a reducing agent e.g., sodium triacetoxyborohydride [NaHB(OAc) 3 , 1.5 to 3 eq.].
  • a compound of Formula-2A e.g., 3,5-dimethoxy-4-formyl phenoxy polystyrene is added to the foregoing solution to form a mixture.
  • This mixture is agitated for up to 18 hours forming a compound of Formula-3.
  • This compound is isolated, washed in succession with DMF (x2), MeOH (x3), DMF (xl), DCM (x2), MeOH (x2), DCM (x2) and Et 2 O (x2) and
  • Compounds of Formula-3 can also be prepared by treating compounds of Formula-1 with SS-CH ⁇ -X, a compound of Formula-2B.
  • This procedure comprises treating an inert solvent, e.g., THF, mixture of a compound of Formula-1 (about 1 to about 1.5 eq.) and a base, e.g., DIPEA (about 1.5 to about 3 eq.), with a mixture of a compound of Formula-2b (1 eq.) in an inert solvent, e.g., THF.
  • This mixture is agitated from about 8 to about 16 hours.
  • the resulting solids are isolated and washed in succession with THF (x3), DCM (x3), MeOH (x3) and DCM (x3) and dried to yield a compound of Formula-3.
  • Synthesis of compounds of Formula I can be accomplished using the following general procedure.
  • Chloranil test indicating the presence of secondary amines, the preceding procedure is repeated until all the secondary amine (compound of Formula-I) is consumed.
  • the optional synthesis of compounds of Formula I is accomplished by treating a compound of Formula-6, where R 4a represents an amino acid protecting group, with a deprotecting agent to yield compounds of Formula-9.
  • This procedure essentially comprises treating an inert solvent mixture, preferably a THF mixture, of a compound of Formula-6 with a deprotecting agent, e.g., piperidine at a temperature of from about 25°C to about 100°C.
  • This step essentially comprises treating compounds of Formula-6 or Formula- 9 with a strong acid solution, preferably a 20% TFA solution in DCM, for up to 30 minutes.
  • a strong acid solution preferably a 20% TFA solution in DCM
  • Compounds of Formula-6 can also be prepared by combining a mixture of a compound of Formula-B ( 2 to 10 eq. wrt to the compound of Formula-A), DIPEA (2- 10 eq. wrt to Formula-A) and HATU (2 to 10 eq. wrt to Formula-A) in a DMF:DCM solvent system with a secondary amine i.e., a compound of Formula-A.
  • This resulting reaction mixture is agitated for 2-12 hours and the resulting solids are isolated. These isolated solids are washed in succession with DMF (x3), MeOH (xl) and DCM (x3).
  • a chloranil test which detects presence of secondary amines, was performed on the washed solids.
  • Scheme IV describes the preparation of a compound of Formula-1, which are used as a starting material in the process of the present invention.
  • L 4-methyl-2-oxo-2H-chromen-7-ylamino, 2-oxo-4-trifluoromethyl-2H- chromen-7-ylamino, 4-methoxycarbonylmethyl-2-oxo-2H-chromen-7-ylamino, 2- oxo-4-(2-oxo-ethyl)-2H-chromen-7-ylamino, 2-oxo-2H-chromen-7-ylamino, 4- nitro-phenylamino, 5-dimethylsulfamoyl-naphthalen-l -ylamino, naphthalen-1 - ylamino, 5-methoxy-naphthalen-l -ylamino, or rhodamino.
  • the first method comprises treating 7-amino-4-methyl-chromen-2-one (L-H, AMC) with a Fmoc protected amino acid, in the presence of IBC and NMM. This method is described in detail by Zimmerman et al, in Anal. Biochem, 1977, 78, 47-51.
  • the second method comprises treating 7-amino-4-methyl-chromen-2-one (L-H, AMC) with a Boc protected amino acid, in the presence of POCl 3 and pyridine. This method is described by Alves et al, in Peptide Res. 1996, 9, 92-96.
  • the protecting groups, Fmoc and Boc, used above can be removed under basic (piperidine/DMF) or acidic (TFA/TES/DCM) deprotecting conditions known to one skilled in the art.
  • the L-Phe(CH,SS) resin (Formula-3; 600 mg, 0.45 mmol) was added to a solution of FmocAla-OH (Formula-4; 841 mg, 2.70 mmol), HATU (1.03 mg, 2.7 mmol), and DIPEA (0.94 ⁇ L, 5.4 mmol) in 1:9/DMF:DCM solvent system and agitated for about 3 hours.
  • the resin was isolated and washed in succession with DMF (x3), MeOH (xl) and DCM (x3) to yield L-Phe-(CH 2 SS)-Ala-Fmoc, a compound of Formula I.
  • the compound of Formula-5 (L-Phe(CH 2 SS)-Ala-H), was coupled with Fmoc-Lys(Boc)-OH (a compound of Formula-4) (709 mg; 1.51 mmol) in the presence of PyBOP (786 mg; 151 mmol) and HOBt (408 mg; 3.02 mmol) in DMF (4 mL) by agitating the mixture for about an hour.
  • the resulting resin was isolated and washed in succession with DMF (x3), MeOH (xl) and DCM (x3) to yield a compound of Formula-6.
  • This step comprised treating L-Phe(CH 2 SS)-Ala-Lys(Boc)-H (a compound of Formula-9) or L-Ph CIi j SS Ala-Lys-Fmoc (a compound of Formula-6) with a 30% TFA solution in DCM for 30 minutes.
  • the reaction solids were isolated and the filtrate was concentrated to yield L-Phe-Ala-Lys-H as a TFA salt.
  • L-Phe-Ala-Lys-Ac (Formula II)
  • the compound of Formula-5 (L-Phe(CH 2 SS)-Ala-H), was coupled with Fmoc-Lys(Boc)-OH (a compound of Formula-4) (709 mg; 1.51 mmol) in the presence of PyBOP (786 mg; 151 mmol) and HOBt (408 mg; 3.02 mmol) in DMF (4 mL) by agitating the mixture for about an hour.
  • the resulting resin was isolated and washed in succession with DMF (x3), MeOH (xl) and DCM (x3) to yield a compound of Formula-6.
  • the reaction solids were isolated and re-treated with a fresh l:4/piperi dine: DMF mixture. This procedure was repeated three times.
  • the resulting resin was isolated and washed with DMF
  • the compound of Formula-9 from above, was treated with a mixture of Ac 2 O, a compound of Formula-12, and DMAP (3 mg) in DCM (3 mL) for about 1.5 hours.
  • This step comprised treating L-Phe(CH 2 SS)-Ala-Lys(Boc)-Ac, a compound of Formula-6, with a 30% TFA solution in DCM for 30 minutes.
  • the reaction solids were isolated by filtration and the filtrate was concentrated to yield L-Phe-Ala-Lys- Ac, Formula II, as a TFA salt.
  • array of compounds indicates a collection of independent
  • array of compounds indicates a collection of individual compounds that are structurally distinct from one another. Also included in the array (library) of compounds is a mixture of the individual compounds.
  • library of compounds can be interchangeably used with the term 'array of compounds.
  • amino acid protecting group represents a group which renders the amino group of the amino acid inactive. Thus when the amine group of the amino acid is protected using a protecting group, the amino group is not capable of reacting, i.e. forming a covalent bond, with any other chemical moiety.
  • the amino acid protecting groups are generally removed by procedures known to one skilled in the art. Illustrative deprotecting procedures comprise treatment with acids or bases or fluoride ions or transition metals, hydrogenation or photochemical treatment.
  • protecting groups are t-butyl carbamate (Boc), fluorenylmethyl carbamate (Fmoc), allyl carbamate (Alloc), benzyl carbamate (CBZ), 2-(trimethylsilyl)ethyl carbamate (Teoc); 2,2,2-trichloroethyl carbamate (Troc), and nitrovateryl (Nvoc).
  • fluorescent moiety (L) represents a chemical moiety capable of fluorescing by absorbing UV radiation between about 300-500 nm.
  • Representative examples of “fluorescent moiety (L)” are 4-methyl-2-oxo-2H- chromen-7-ylamino, 2-oxo-4-trifluoromethyl-2H-chromen-7-ylamino, 4- methoxycarbonylmethyl-2-oxo-2H-chromen-7-ylamino, 2-oxo-4-(2-oxo-ethyl)-2H- chromen-7-ylamino, 2-oxo-2H-chromen-7-ylamino, 4-nitro-phenylamino, 5- dimethylsulfamoyl-naphthalen-1-ylamino, naphthalen-1 -ylamino, 5-methoxy- naphthalen-l -ylamino, and rhodamino.
  • reducing agent is meant to represent a group capable of donating one or two electrons or a hydride.
  • Illustrative examples are NaBH(OAc) 3 , diborane, BH j .pyridine, BH 3 .dimethylsulfide, BH 3 .THF, NaBH 4 , NaCNBH 3 , Zn(BH 4 ) 2 and LiBH 4 .
  • LG or “leaving group” is as understood by one skilled in the art, and is intended to represent a group that will be replaced by another group which generally acts as a nucleophile. A detailed description of leaving groups can be found in Organic Chemistry, K. P. C Vollhardt, 1987.
  • Illustrative examples of leaving groups are halogen (Cl, I, Br, and F), tosylate, mesylate, and triflate.
  • the "acid” used to treat the compound of Formula II, wherein R 5 represents an amino acid protecting group to yield a compound of Formula II wherein R 5 represents H usually functions as a deprotecting agent.
  • this acid is selected from a group consisting of alkyl or aryl sulfonic acids, TFA, HC1, HNO 3 , H j SO, and HF.
  • Solid support signifies polymeric material for supported synthesis. Solid support should be acid labile, photochemically cleavable to facilitate formation of a compound of Formula I, and should be chemically stable under the conditions of the present process.
  • SS are 3,5-dimethoxy-4-formylphenoxy polystyrene, 2-(3,5-dimethoxy-4-formylphenoxy)ethoxy- methyl polystyrene, 2-(3,5-dimethoxy-4- formylphenoxy)ethyl polystyrene, 4-(3,5-dimethoxy-4- formylphenoxy)butyramidomethyl polystyrene, 4-(3,5-dimethoxy-4- formylphenoxy)propionamidomethyl polystyrene, and 4-(3,5-dimethoxy-4- formylphenoxy)acetamidomethyl polystyrene (all collectively known as PALS).
  • PALS 4-(3,5-dimethoxy-4- formylphenoxy)acetamidomethyl polystyrene
  • deprotecting agent is used to mean an agent which selectively removes a PG from a functional group such as an amine group.
  • the deprotecting agent can be an acidic or basic moiety as understood by one skilled in the art.
  • protecting group or "PG”, as used herein, indicates a group that protects an amine functional group rendering the amine inactive.
  • a detailed description of the terms “deprotecting agent”, and “protecting group” (PG) is available in Protective Groups in Organic Synthesis, 2nd edition, T. W. Greene and P. G. M. Wuts, 1991, which is incorporated herein by reference.
  • Suitable Solvent as used herein is meant to indicate a solvent which is compatible with reducing conditions and able to swell the solid support (SS).
  • suitable solvent are THF, dioxane, toluene, dimethyl formamide (DMF), dimethyl sulfoxide (DMSO), dimethyl acetamide (DMA), dichloro methane (DCM), N-methyl pyrrolidinone (NMP) or mixtures thereof.
  • suitable solvents can be found in Tet. Lett. 1998, 39, 8451-54, and is incorporated herein by reference.
  • Alkyl or “alkyl radical” is meant to indicate a saturated or partially unsaturated hydrocarbon moiety containing 1 to 14 carbon atoms. This hydrocarbon moiety is generally attached to at least one other atom, and can be straight chain, or branched, or cyclic.
  • An example of a partially unsaturated hydrocarbon moiety is an "alkelene" group which has at least one center of unsaturation, i.e., a double bond.
  • Illustrative examples are butene, butadiene, propene, and pentene.
  • a cyclic hydrocarbon moiety is represented by "cycloalkyl", “cycloalkyl ring", or “cycloalkyl radical” which can be saturated or partially unsaturated three to ten carbon monocyclic or bicyclic hydrocarbon moiety which is optionally substituted with an R 7 and R 8 groups.
  • the term straight chain alkyl is meant to represent an unbranched hydrocarbon moiety of up to 8 carbon atoms.
  • An example of a straight chain alkyl is a n-pentyl group.
  • aryl means an aromatic monocyclic, bicyclic, or a fused polycyclic hydrocarbon radical containing the number of carbon atoms indicated.
  • a C 6 -C 14 aryl group includes phenyl, naphthyl, anthracenyl, etc.
  • heteroaryl means aryl, as defined above, wherein one or more of the carbon atoms is replaced by a hetero atom chosen from N, O, and S.
  • the hetero atoms can exist in their chemically allowed oxidation states.
  • Sulfur (s) can exist as a sulfide, sulfoxide, or sulfone.
  • Each heteroaryl ring comprises from five (5) to fourteen (14) atoms.
  • heteroaryl groups are thienyl, furyl, pyrrolyl, indolyl, pyrimidinyl, isoxazolyl, purinyl, imidazolyl, pyridyl, pyrazolyl, quinolyl, and pyrazinyl.
  • hetero cyclic ring means cycloalkyl, as defined above, except one or more of the carbon atoms of the cycloalkyl group are replaced by a hetero atom chosen from N, NR 12 , O , S(O), S(O) 2 and S, wherein R 12 is (C 1 6 )alkyl or hydrogen.
  • hetero cycloalkyl are morpholinyl, indolinyl, piperidyl, pyrrolidinyl, pyrrolinyl, imidazolidinyl, quinuclidinyl and morpholinyl.
  • amino acid represents a natural or unnatural amino acid.
  • natural amino acid as used herein is intended to represent the twenty naturally occurring amino acids in their L' form, which are some times also referred as 'common amino acids', a list of which can be found in Biochemistry, Harper & Row Publishers, Inc. (1983).
  • unnatural amino acid as used herein, is intended to represent the 'D' or 'DL' forms of the twenty naturally occurring amino acids described above. It is further understood that the term unnatural amino acid includes homologues of the natural amino acids, and synthetically modified form of the natural amino acids.
  • the synthetically modified forms include amino acids having alkylene chains shortened or lengthened by up to two carbon atoms, amino acids comprising optionally substituted aryl groups, and amino acids having halogenated groups, preferably halogenated alkyl and aryl groups. Additional description of the term "amino acid” can be found in US Patent Numbers 5,514,694 and 5, 610,297, and BaChem Chemicals Catalog (1999) which are all incorporated herein by reference.
  • N-natural amino acid side chain substituent and "N- unnatural amino acid side chain” substituent is a group wherein the nitrogen atom (N) is the annular ring atom substituted with a natural or unnatural amino acid side chain (natural or unnatural amino acid side chain is a defined above).
  • protected natural amino acid represents an amino acid, as defined above, wherein the amino group and/or the side chain of the amino acid is protected with an amino acid protecting group.
  • protected unnatural amino acid represents an unnatural amino acid, as defined earlier, wherein the amine group of the unnatural amino acid or its side chain is protected with an amino acid protecting group.
  • the term “varied structural order” as used herein is intended to explain the structural arrangement of the peptide or peptidal derivatives represented by, for example, Formula II in the present invention. Thus a compound or compounds of Formula II which comprise amino acid components can have these amino acid components arranged in any order such that the compounds of Formula II have a diverse or varied structural order thereby making these compounds distinct from one another.
  • R 7 and R 8 Optional substituents for aryl, hetero aryl, and Ph groups are R 7 and R 8 . These R 7 substituents at each occurrence are independently selected from a group consisting of H, NH,, halo, O-C alkyl, NHC,-C 4 alkyl, N(C,-C 4 ) 2 alkyl, and CF 3 ; while R 8 is selected from H and C M alkyl.
  • BH j .dimethylsulfide borane dimethyl sulfide complex
  • BH j .THF borane tetrahydrofuran complex
  • DIPCDI diisopropylcarbodiimide
  • DIPEA diisopropylethylamine
  • HATU O-(7-azabenzotriazo- 1 -yl)- 1,1,3 ,3-tetramethyluronium hexafluorophosphate
  • NMM N-methyl morpholine
  • POCl 3 phosphorous oxychloride
  • TES triethyl silane
  • TFA trifluoroacetic acid
  • THF tetrahydrofuran
  • TMSC1 chlorotrimethylsilane wrt: with respect to

Abstract

The present invention provides a process for synthesizing a compound or an array of compounds of Formula (I) and Formula (6) wherein peptidal substrates are bound to a solid support and a fluorescent moiety. Also provided is a process for synthesizing compounds of Formula (II) wherein peptidal substrates are bound to a fluorescent moiety. These related processes afford said peptidal substrates having a varied structural order.

Description

SYNTHESIS OF PROTEASE SUBSTRATES
FIELD OF INVENTION
The present invention relates to synthesis of protease substrates. These protease substrates typically are peptide(s) or peptide derivative(s) covalently bound to a fluorescent moiety precursor (L) or an array of the same.
BACKGROUND OF THE INVENTION
Assays for determining enzymatic activity, enzyme inhibition, agonists and antagonists of biological processes are of great interest and are very useful in the pharmaceutical industry.
One such assay uses protease substrates, i.e., peptides or peptide derivatives covalently bound to a fluorescent moiety through an amide or an ester bond. Enzymes, including proteases, having affinity for peptides or peptide derivatives cleave the bond between the peptide or peptide derivative and the fluorescent moiety, thereby releasing the fluorescent moiety. Spectroscopic detection/measurement of the release of the fluorescent moiety is then used to determine the structural characteristics of the binding peptide and also the level of such a binding to a given enzyme.
The foregoing technology was first reported in 1976 by Zimmerman et al., in Anal. Biochem., 1976, 70, 258-262, wherein the fluorescent 7-amino-4-methyl- chromen-2-one (AMC) precursor, i.e., 4-methyl-2-oxo-2H-chromen-7-ylamino, was covalently bound to a peptide which was then assayed against Chymotrypsin. Fluorometric detection of AMC was then used to determine chymotrypsin activity.
Little is known about structures, active sites and binding affinity of enzymes such as proteases. Screening known substrates against these enzymes is one tool that is used to study characteristics of these enzymes. Screening however does not always yield results that shed light on the enzyme structure. Synthesizing substrates having a varied structural order is a more efficient way to learn and understand enzymes such as proteases.
At the present time no convenient method is available for synthesizing substrates having a varied structural order and which are attached to a fluorescent moiety. Given the utility of peptidal substrates bound to fluorescent moieties, there is a need for a process which will afford such peptidal substrates having a varied structural order.
SUMMARY OF THE INVENTION Keeping the above discussed needs in mind the present invention provides a process for synthesizing a compound or an array of compounds of Formula I and Formula-6 wherein peptidal substrates are bound to a solid support and a fluorescent moiety. Also provided is a process for synthesizing for synthesizing compounds of Formula II wherein peptidal substrates are bound to a fluorescent moiety. These related processes afford said peptidal substrates having a varied structural order. The present invention also provides novel compounds of Formula-3 which are useful in the processes of the present invention.
DETAILED DESCRIPTION OF THE INVENITON
The present invention provides a process for synthesizing a compound or an array of compounds of Formula I:
Figure imgf000004_0001
wherein:
R1 represents a protected or unprotected natural or unnatural amino acid side chain; R2 represents a protected or unprotected natural or unnatural amino acid side chain;
R3 represents H or C1 4-alkyl; alternatively
R2 and R3 along with the carbon and nitrogen atom to which they are attached form a five to ten membered hetero cyclic ring; R4 represents R4a or H;
R4a represents R5, SO2-R!0 , CO-OR10, C(O)-NH-R10, C(S)-NH-R10, C(O)-R10 or C(S)-
R'°;
L represents a fluorescent moiety;
SS represents a solid support; R5 represents an amino acid protecting group; and
R10 represents H, aryl, (CH2)1 6 aryl, (CH,)0.6 heteroaryl, C,_8 alkyl, C4 14 branched alkyl or C^ cycloalkyl; the process comprising the steps of
(i) reacting, in a suitable solvent, a primary amine of Formula- 1
Figure imgf000005_0001
Formula-1,
with either:
(a) a compound of Formula-2A
SS-CHO Formula-2A,
in the presence of a reducing agent, or
(b) a compound of Formula-2B,
SS-CHj-X Formula-2B, to form a secondary amine of Formula 3
Figure imgf000006_0001
.Formula-3,
where L, SS and R1 are as defined above and X is a leaving group;
(ii) treating the secondary amine of Formula-3, with a compound of Formula-4
Figure imgf000006_0002
.Formula-4,
to form a compound of Formula-I, where R4 represents R4a, and R2, R3 and R4a are as defined above, to form a compound of Formula I; and
(iii) optionally treating a compound of Formula I, where R4a represents R5, with a deprotecting agent to form a compound of Formula I, where R4 represents H.
Preferred embodiments of the present invention provide a process wherein L represents a fluorescent moiety selected from 4-methyl-2-oxo-2H-chromen-7- ylamino, 2-oxo-4-trifluoromethyl-2H-chromen-7-ylamino, 4- methoxycarbonylmethyl-2-oxo-2H-chromen-7-ylamino, 2-oxo-4-(2-oxo-ethyl)-2H- chromen-7-ylamino, 2-oxo-2H-chromen-7-ylamino, 4-nitro-phenylamino, 5- dimethylsulfamoyl-naphthalen-1 -ylamino, naphthalen-1 -ylamino, 5-methoxy- naphthalen-1 -ylamino, and rhodamino; and SS represents a solid support selected from PALS. Another preferred embodiment provides a process wherein the reducing agent in step (i)(a) is selected from NaBH(OAc)3, diborane, BH3.pyridine, BH3.dimethylsulfide, BH3.THF, NaBH4, NaCNBH3, Zn(BH4)2 and LiBH4. A further preferred embodiment provides a process wherein L represents 4-methyl-2-oxo-2H-chromen-6-ylamino. Another aspect of the present invention provides a process for synthesizing a compound or an array of compounds of Formula II
Figure imgf000007_0001
Formula II wherein:
R represents a protected or unprotected natural or unnatural amino acid side chain;
R2 independently at each occurance represents a protected or unprotected natural or unnatural amino acid side chain;
R3 independently at each occurance represents H or C -alkyl; alternatively R2 and R3 independently at each occurance along with the carbon and nitrogen atom to which they are attached form a five to ten membered hetero cyclic ring;
R4 represents R4a or H;
R4a represents R5, SO2-R10 , CO-OR10, C(O)-NH-R10, C(S)-NH-R10, C(O)-R10 or C(S)-
R10; L represents a fluorescent moiety;
R5 represents an amino acid protecting group;
R10 represents H, aryl, (CH,)1 6 aryl, (CH^ heteroaryl, C,.g alkyl, C4 14 branched alkyl or C^ cycloalkyl; and
"n" represents an integer from 1 to 7; said process comprising
(a) treating a compound of Formula-5
Figure imgf000007_0002
.Formula-5 where R1, R2 and R3 are as defined above, SS represents a solid support, and "q" represents an integer from about 0 to 6, with a compound of Formula-4
Figure imgf000008_0001
.Formula-4
where R , R and R a are as defined above, to form a compound of Formula-6
Figure imgf000008_0002
.Formula-6
where R1, R2, R3, R4\ SS, "n" and L are as defined above;
(b) optionally treating a compound of Formula-6, when R4a = R5, with a deprotecting agent to form a compound of Formula-9
Figure imgf000008_0003
.Formula-9
where R1, R2, R3, SS, "n" and L are as defined above; and
(c) treating a compound of Formula-6 or a compound of Formula-9 with a strong acid to yield a compound of Formula II.
Yet another related process of the present invention provides a process for synthesizing a compound or an array of compounds of Formula II
Figure imgf000009_0001
Formula II wherein:
R1 represents a protected or unprotected natural or unnatural amino acid side chain;
R2 independently at each occurance represents a protected or unprotected natural or unnatural amino acid side chain;
R3 independently at each occurance represents H or C,_4-alkyl; alternatively
R2 and R3 independently at each occurance along with the carbon and nitrogen atom to which they are attached form a five to ten membered hetero cyclic ring;
R4 represents R4a or H; R4a represents R5, SO2-R10 , CO-OR10, C(O)-NH-R10, C(S)-NH-R10, C(O)-R10 or C(S)-
R10;
L represents a fluorescent moiety;
R5 represents an amino acid protecting group;
R10 represents H, aryl, (CH,),.,; aryl, (CH,)^ heteroaryl, C1 8 alkyl, C4.14 branched alkyl or ,_14 cycloalkyl; and
"n" represents an integer from 1 to 7; said process comprising
(a) treating a compound of Formula-6 when R4a = R5,
Figure imgf000009_0002
Formula-6
with a deprotecting agent to form a compound of Formula-9
Figure imgf000010_0001
.Formula-9
where R1, R2, R3, SS, "n" and L are as defined above;
(b) treating a compound of Formula-9 with a compound of Formula- 12
R a-X Formula-12
where R4a is as defined above, to form a compound of Formula-6; and
(c) treating a compound of Formula-6 or a compound of Formula-9 with a strong acid to yield a compound of Formula II.
In a preferred embodiment of the process to synthesize a compound or an array of compounds of Formula II L represents a fluorescent moiety selected from 4- methyl-2-oxo-2H-chromen-7-ylamino, 2-oxo-4-trifluoromethyl-2H-chromen-7- ylamino, 4-methoxycarbonylmethyl-2-oxo-2H-chromen-7-ylamino, 2-oxo-4-(2- oxo-ethyl)-2H-chromen-7-ylamino, 2-oxo-2H-chromen-7-ylamino, 4-nitro- phenylamino, 5-dimethylsulfamoyl-naphthalen-l -ylamino, naphthalen-1 -ylamino, 5-methoxy-naphthalen-l -ylamino, and rhodamino; and SS represents a solid support selected from PALS. In a particularly preferred embodiment L represents 4- methyl-2-oxo-2H-chromen-6-ylamino. Another aspect of the present invention provides a process synthesizing a compound or an array of compounds of Formula-6
Figure imgf000010_0002
.Formula-6
wherein R1 represents a protected or unprotected natural or unnatural amino acid side chain;
R2 independently at each occurance represent a protected or unprotected natural or unnatural amino acid side chain;
R3 independently at each occurance represents H or C1 4-alkyl; alternatively
R2 and R3 independently at each occurance along with the carbon and nitrogen atom to which they are attached form a five to ten membered hetero cyclic ring;
R4 represents R4a or H;
R4a represents R5, SO2-R10 , CO-OR10, C(O)-NH-R10, C(S)-NH-R10, C(O)-R10 or C(S)-
R10;
L represents a fluorescent moiety;
SS represents a solid support;
R5 represents an amino acid protecting group;
R10 represents H, aryl, (CH,^ heteroaryl, (CHj),^ aryl, C1 8 alkyl, C4 14 branched alkyl, or ^ cycloalkyl; and
"n" represents an integer from 1 to 7; the process comprising treating a compound of Formula A
Figure imgf000011_0001
.Formula A
with a compound of Formula B
Figure imgf000011_0002
.Formula B where R1, R2, R3, R4a, L and SS are as defined above, and "v" represents an integer of from 1 to 5, to form a compound of Formula-6.
Another aspect of the present invention provides a compound of Formula-3
Figure imgf000012_0001
.Formula-3,
wherein:
R1 represents a protected or unprotected natural or unnatural amino acid side chain;
L represents a fluorescent moiety; and SS represents a solid support. Preferred compounds of Formula-3 are those wherein L represents a fluorescent moiety selected from 4-methyl-2-oxo-2H-chromen-7-ylamino, 2-oxo-4- trifluoromethyl-2H-chromen-7-ylamino, 4-methoxycarbonylmethyl-2-oxo-2H- chromen-7-ylamino, 2-oxo-4-(2-oxo-ethyl)-2H-chromen-7-ylamino, 2-oxo-2H- chromen-7-ylamino, 4-nitro-phenylamino, 5-dimethylsulfamoyl-naphthalen-l- ylamino, naphthalen-1 -ylamino, 5-methoxy-naphthalen-l -ylamino, and rhodamino.
Experimental Details
The present invention is further described in the schemes outlined below. Starting materials used in the present invention are available from commercial sources such as Aldrich Chemicals, Sigma and BaChem. Compounds of the present invention or those referred to in the present invention were named using Beilstein AutoNom, Version 2.0, which is part of Beilstein Commander, Version 2.0, 1995-1996, Beilstein Informationssysteme GmbH. Outlined in Scheme I is novel process for synthesizing compounds of Formula
I: Scheme I
Figure imgf000013_0001
Figure imgf000013_0002
Formula I
Depicted in Scheme II, below, is the process for the synthesis of compounds of Formula II:
Scheme II
coupling agent
Figure imgf000014_0001
Formula-5 Formula-4
Figure imgf000014_0002
Figure imgf000014_0003
Scheme III: Alternate Synthesis of Formula-6 Compounds
Figure imgf000015_0001
Formula-A
Formula-B (v = 1-5)
Figure imgf000015_0002
General Procedure:
The process of the present invention is generally discussed below.
Compounds of Formula I (Scheme I):
Synthesis of Compounds of Formula-3
Synthesis of compounds of Formula-3 can be accomplished by the procedure of Boojamra, C. G.; Burow, K. M.; Thompson, L. A.; Ellman, J. A. J. Org. Chem. 1997, 62, 1240-1256. A general procedure is discussed below.
A suspension/mixture of an acid salt of a compound of Formula-1 (1.5 eq. wit to a compound of Formula- 2A) and a 2 % AcOH solution in DMA is combined with a reducing agent, e.g., sodium triacetoxyborohydride [NaHB(OAc)3, 1.5 to 3 eq.]. The resulting mixture is agitated to form a solution. A compound of Formula-2A, e.g., 3,5-dimethoxy-4-formyl phenoxy polystyrene is added to the foregoing solution to form a mixture. This mixture is agitated for up to 18 hours forming a compound of Formula-3. This compound is isolated, washed in succession with DMF (x2), MeOH (x3), DMF (xl), DCM (x2), MeOH (x2), DCM (x2) and Et2O (x2) and dried.
Compounds of Formula-3 can also be prepared by treating compounds of Formula-1 with SS-CH^-X, a compound of Formula-2B. This procedure comprises treating an inert solvent, e.g., THF, mixture of a compound of Formula-1 (about 1 to about 1.5 eq.) and a base, e.g., DIPEA (about 1.5 to about 3 eq.), with a mixture of a compound of Formula-2b (1 eq.) in an inert solvent, e.g., THF. This mixture is agitated from about 8 to about 16 hours. The resulting solids are isolated and washed in succession with THF (x3), DCM (x3), MeOH (x3) and DCM (x3) and dried to yield a compound of Formula-3.
Synthesis of a Compound of Formula-I
Synthesis of compounds of Formula I can be accomplished using the following general procedure. A mixture of a compound of Formula-4 ( 2 to 10 eq. wrt to the compound of Formula-3), DIPEA (2-10 eq. wrt to Formula-3) and HATU (2 to
10 eq. wrt to Formula-3) in a DMF:DCM solvent system is combined with a secondary amine i.e., a compound of Formula-3. This resulting reaction mixture is agitated for 2-12 hours and the resulting solids are isolated. These isolated solids are washed in succession with DMF (x3), MeOH (xl) and DCM (x3). A chloranil test, which detects presence of secondary amines, is performed on the washed solids.
(Details of the Chloranil test can be found in Novabiochem Catalog synthesis notes pS43 (1999), which are incorporated herein by reference.) In the event of a positive
Chloranil test, indicating the presence of secondary amines, the preceding procedure is repeated until all the secondary amine (compound of Formula-I) is consumed.
Compounds of Formula II (Scheme II)
Synthesis of Compounds of Formula-6, where n = 1-7 Compounds of Formula-6 (where n = 2-7) can be synthesized by treating a mixture of a compound of Formula-4 ( 2 to 10 eq. wrt to the compound of Formula- 5), DIPEA (2-10 eq. wrt to Formula-3) and HATU (2 to 10 eq. wrt to Formula-5) in a DMF:DCM solvent system with a secondary amine i.e., a compound of Formula-5. This resulting reaction mixture is agitated for 2-12 hours and the resulting solids are isolated. These isolated solids are washed in succession with DMF (x3), MeOH (xl) and DCM (x3) to yield a compound of Formula-6.
Compounds of Formula-9
The optional synthesis of compounds of Formula I is accomplished by treating a compound of Formula-6, where R4a represents an amino acid protecting group, with a deprotecting agent to yield compounds of Formula-9. This procedure essentially comprises treating an inert solvent mixture, preferably a THF mixture, of a compound of Formula-6 with a deprotecting agent, e.g., piperidine at a temperature of from about 25°C to about 100°C.
Synthesis of Compounds of Formula II
This step essentially comprises treating compounds of Formula-6 or Formula- 9 with a strong acid solution, preferably a 20% TFA solution in DCM, for up to 30 minutes. The solids are isolated and the filtrate concentrated to yield a compound of Formula II.
Alternate Synthesis of Formula-6 Compounds (Scheme III)
Compounds of Formula-6 can also be prepared by combining a mixture of a compound of Formula-B ( 2 to 10 eq. wrt to the compound of Formula-A), DIPEA (2- 10 eq. wrt to Formula-A) and HATU (2 to 10 eq. wrt to Formula-A) in a DMF:DCM solvent system with a secondary amine i.e., a compound of Formula-A. This resulting reaction mixture is agitated for 2-12 hours and the resulting solids are isolated. These isolated solids are washed in succession with DMF (x3), MeOH (xl) and DCM (x3). A chloranil test, which detects presence of secondary amines, was performed on the washed solids. (Details of the Chloranil test can be found in Novabiochem Catalog synthesis notes pS43 (1999), which are incorporated herein by reference.) In the event of a positive Chloranil test, indicating the presence of secondary amines, the preceding procedure is repeated until all the secondary amine (compound of Formula- A) is consumed.
Compounds Of Formula-1
Scheme IV describes the preparation of a compound of Formula-1, which are used as a starting material in the process of the present invention.
Scheme IV
IBCNMM
Figure imgf000018_0001
POCl3/Pyridιne
Figure imgf000018_0003
Figure imgf000018_0002
L = 4-methyl-2-oxo-2H-chromen-7-ylamino, 2-oxo-4-trifluoromethyl-2H- chromen-7-ylamino, 4-methoxycarbonylmethyl-2-oxo-2H-chromen-7-ylamino, 2- oxo-4-(2-oxo-ethyl)-2H-chromen-7-ylamino, 2-oxo-2H-chromen-7-ylamino, 4- nitro-phenylamino, 5-dimethylsulfamoyl-naphthalen-l -ylamino, naphthalen-1 - ylamino, 5-methoxy-naphthalen-l -ylamino, or rhodamino.
Compounds of Formula-1 can be synthesized by methods known to one skilled in the art. Two such methods are depicted in Scheme IV above.
The first method comprises treating 7-amino-4-methyl-chromen-2-one (L-H, AMC) with a Fmoc protected amino acid, in the presence of IBC and NMM. This method is described in detail by Zimmerman et al, in Anal. Biochem, 1977, 78, 47-51. The second method comprises treating 7-amino-4-methyl-chromen-2-one (L-H, AMC) with a Boc protected amino acid, in the presence of POCl3 and pyridine. This method is described by Alves et al, in Peptide Res. 1996, 9, 92-96.
The protecting groups, Fmoc and Boc, used above can be removed under basic (piperidine/DMF) or acidic (TFA/TES/DCM) deprotecting conditions known to one skilled in the art.
Examples:
Listed below are examples of compounds of Formula I that were prepared using the process of the present invention. L-Phe(CH2SS)-Ala-Fmoc L-Ala(CH2SS)-Phe-Fmoc L-Phe(CH2SS)-Gly-Fmoc L-Phe(CH2SS)-His(Boc)-Fmoc L-Ala(CH2SS)-Pro-Fmoc L-Ala(CH2SS)-Leu-Fmoc L-Lys(CH2SS)-Ala-Fmoc L-Phe(CH2SS)-Orn-Fmoc
(L = 4-methyl-2-oxo-2H-chromen-7-ylamino)
L-Phe(CH2SS)-Ala-Fmoc (Formula I):
Synthesis of L-Phe(CRSS) (Formula-3
A mixture of a HC1 (or TFA) salt of L-Phe-H (Formula-1) (1.78 g, 4.95 mmol), a 2% AcOH solution in dry DMA (30 mL) and pulverized NaHB(OAc)3 (15 mmol) was agitated to form a solution. This solution then was combined with 3,5- dimethoxy-4-formylphenoxy polystyrene ("PAL" resin (SS-CHO, Formula-2A), 3.0g, 1.1 mmol/g.) The reaction mixture was agitated from about 8 to about 16 hours. The resin was isolated and washed in succession with DMF (x6), MeOH (x3), DMF (xl), DCM (x2), MeOH (x2), DCM (x2) and Et2O (xl). The washed resin was dried to yield L-Phe(CIi,SS), a compound of Formula-3. Synthesis of L-PhefCFtSSVAla-Fmoc (Formula I)
The L-Phe(CH,SS) resin (Formula-3; 600 mg, 0.45 mmol) was added to a solution of FmocAla-OH (Formula-4; 841 mg, 2.70 mmol), HATU (1.03 mg, 2.7 mmol), and DIPEA (0.94 μL, 5.4 mmol) in 1:9/DMF:DCM solvent system and agitated for about 3 hours. The resin was isolated and washed in succession with DMF (x3), MeOH (xl) and DCM (x3) to yield L-Phe-(CH2SS)-Ala-Fmoc, a compound of Formula I.
L-Phe-Ala-Lys-H (Formula II)
Synthesis of L-Phe(CH.SS)-Ala-Lvs(Boc)-Fmoc (Formula 6)
The compound of Formula-5, (L-Phe(CH2SS)-Ala-H), was coupled with Fmoc-Lys(Boc)-OH (a compound of Formula-4) (709 mg; 1.51 mmol) in the presence of PyBOP (786 mg; 151 mmol) and HOBt (408 mg; 3.02 mmol) in DMF (4 mL) by agitating the mixture for about an hour. The resulting resin was isolated and washed in succession with DMF (x3), MeOH (xl) and DCM (x3) to yield a compound of Formula-6.
Synthesis of L-Phe(CFLSS)-Ala-Lvs(Boc)-H (Formula-9) The L-Phe(CH2SS)-Ala-Lys(Boc)-Fmoc resin(403 mg), from above, was treated with a l:4/piperidine:DMF mixture for about 5 minutes. The reaction solids were isolated and re-treated with a fresh l:4/piperidine:DMF mixture. This procedure was repeated three times. The resulting resin was isolated and washed with DMF (xlO) to yield a compound of Formula-9, i.e. L-Phe(CH2SS)-Ala-Lys(Boc)-H.
Synthesis of L-Phe-Ala-Lys-H (Formula II)
This step comprised treating L-Phe(CH2SS)-Ala-Lys(Boc)-H (a compound of Formula-9) or L-Ph CIijSS Ala-Lys-Fmoc (a compound of Formula-6) with a 30% TFA solution in DCM for 30 minutes. The reaction solids were isolated and the filtrate was concentrated to yield L-Phe-Ala-Lys-H as a TFA salt. L-Phe-Ala-Lys-Ac (Formula II)
Synthesis of L-Phe(CFjSS)-Ala-Lvs-Fmoc (Formula-6)
The compound of Formula-5, (L-Phe(CH2SS)-Ala-H), was coupled with Fmoc-Lys(Boc)-OH (a compound of Formula-4) (709 mg; 1.51 mmol) in the presence of PyBOP (786 mg; 151 mmol) and HOBt (408 mg; 3.02 mmol) in DMF (4 mL) by agitating the mixture for about an hour. The resulting resin was isolated and washed in succession with DMF (x3), MeOH (xl) and DCM (x3) to yield a compound of Formula-6.
Synthesis of L-Phe(CKSS)-Ala-Lvs(Boc)-H (Formula-9)
The L-Phe(CH2SS)-Ala-Lys(Boc)-Fmoc resin(403 mg), from above, was treated with a l:4/piperidine:DMF mixture for about 5 minutes. The reaction solids were isolated and re-treated with a fresh l:4/piperi dine: DMF mixture. This procedure was repeated three times. The resulting resin was isolated and washed with DMF
(xlO) to yield a compound of Formula-9, i.e. L-Phe(CH2SS)-Ala-Lys(Boc)-H.
Synthesis of L-Phe(CRSS)Ala-Lys(Boc)-Ac (Formula-6)
The compound of Formula-9, from above, was treated with a mixture of Ac2O, a compound of Formula-12, and DMAP (3 mg) in DCM (3 mL) for about 1.5 hours.
The resulting resin was isolated and washed in succession with DMF (x3), MeOH
(xl) and DCM (x3) and dried to yield a compound of Formula-6, where R4a represents
COCH3.
Synthesis of L-Phe-Ala-Lys-Ac (Formula II)
This step comprised treating L-Phe(CH2SS)-Ala-Lys(Boc)-Ac, a compound of Formula-6, with a 30% TFA solution in DCM for 30 minutes. The reaction solids were isolated by filtration and the filtrate was concentrated to yield L-Phe-Ala-Lys- Ac, Formula II, as a TFA salt. Physical Data:
The following compounds of Formula II were prepared using the process of the present invention. Standard 1
Figure imgf000022_0001
Analytical data :
'H-NMR: (270 MHz, OMSO-d6) δ : 1.08 (d, 3H), 1.2-1.4 (m, 6H), 2.38 (s, 3H), 2.71
(br s, 2H), 2.93 (dd, IH), 3.07 (dd, IH), 3.97 (m, IH), 4.19 (m IH), 4.25 (m, 3H), 4.62
(m IH), 6.26 (s, IH), 7.10-7.30 (m, 5H), 7.39 (m, 2H), 7.52 (d, IH), 7.60-7.72 (m,
4H), 7.88 (d, 2H), 8.02 (d, IH), 8.22 (d, IH), 10.44 (s, IH).
ESIMS calcd for C43H45N5O7 (M + H)+ m /z 744, found 744.
Standard 2
Figure imgf000022_0002
.TFA
Analytical data:
'H-NMR (270 MHz, DMSO-rf6) δ 1.18 (dd, 3H), 1.31 (m, 2H), 1.50 (m, 4H), 1.60 (m,
2H), 1.83 (d, 3H), 2.40 (s, 3H), 2.70 (br s, 3H), 2.94 (m, IH), 3.06 (m, IH), 4.22 (m,
2H), 4.61 (m, IH), 6.28 (s, IH), 7.20 (m, IH), 7.25 (m, 3H), 7.44 (m, IH), 7.65 (br s,
IH), 7.73 (m, IH), 8.05 (m, IH), 8.17 (m, 1H),10.41 (s, IH).
ESIMS calcd for C30H37N5O6 (M + ΪT)+ m /z 564, found 564. DEFINITIONS
The following terms as used herein have the following meaning, unless indicated otherwise. The term "array of compounds" indicates a collection of independent
(individual) compounds that are synthesized by the process of the present invention. Generally the term array of compounds indicates a collection of individual compounds that are structurally distinct from one another. Also included in the array (library) of compounds is a mixture of the individual compounds. The term "library of compounds" can be interchangeably used with the term 'array of compounds".
The term "amino acid protecting group" as used herein represents a group which renders the amino group of the amino acid inactive. Thus when the amine group of the amino acid is protected using a protecting group, the amino group is not capable of reacting, i.e. forming a covalent bond, with any other chemical moiety. The amino acid protecting groups are generally removed by procedures known to one skilled in the art. Illustrative deprotecting procedures comprise treatment with acids or bases or fluoride ions or transition metals, hydrogenation or photochemical treatment. Illustrative examples of protecting groups are t-butyl carbamate (Boc), fluorenylmethyl carbamate (Fmoc), allyl carbamate (Alloc), benzyl carbamate (CBZ), 2-(trimethylsilyl)ethyl carbamate (Teoc); 2,2,2-trichloroethyl carbamate (Troc), and nitrovateryl (Nvoc).
The term "fluorescent moiety (L)" as used herein represents a chemical moiety capable of fluorescing by absorbing UV radiation between about 300-500 nm. Representative examples of "fluorescent moiety (L)" are 4-methyl-2-oxo-2H- chromen-7-ylamino, 2-oxo-4-trifluoromethyl-2H-chromen-7-ylamino, 4- methoxycarbonylmethyl-2-oxo-2H-chromen-7-ylamino, 2-oxo-4-(2-oxo-ethyl)-2H- chromen-7-ylamino, 2-oxo-2H-chromen-7-ylamino, 4-nitro-phenylamino, 5- dimethylsulfamoyl-naphthalen-1-ylamino, naphthalen-1 -ylamino, 5-methoxy- naphthalen-l -ylamino, and rhodamino. The term "reducing agent" is meant to represent a group capable of donating one or two electrons or a hydride. Illustrative examples are NaBH(OAc)3, diborane, BHj.pyridine, BH3.dimethylsulfide, BH3.THF, NaBH4, NaCNBH3, Zn(BH4)2 and LiBH4. As used in the present invention, the term "LG" or "leaving group" is as understood by one skilled in the art, and is intended to represent a group that will be replaced by another group which generally acts as a nucleophile. A detailed description of leaving groups can be found in Organic Chemistry, K. P. C Vollhardt, 1987. Illustrative examples of leaving groups are halogen (Cl, I, Br, and F), tosylate, mesylate, and triflate. It is understood that the "acid" used to treat the compound of Formula II, wherein R5 represents an amino acid protecting group to yield a compound of Formula II wherein R5 represents H, usually functions as a deprotecting agent. In particular this acid is selected from a group consisting of alkyl or aryl sulfonic acids, TFA, HC1, HNO3, HjSO, and HF.
The term "optional" or "optionally" means that the subsequently described event or circumstance may or may not occur, and that the description includes instances where the event or circumstance occurs and instances in which it does not. For example, the phrase "optionally is substituted with one to three substituents" means that the group referred to may or may not be substituted in order to fall within the scope of the invention. Thus the term "optionally substituted" is intended to mean that any one or more hydrogens on a designated atom can be replaced with a selection from the indicated group, provided that the designated atom's normal valence is not exceeded, and that the substitution results in a stable compound. When the substituent is keto (=O) then 2 hydrogens on the atom are replaced. As used in the present invention, the illustration:
generally indicates a point of attachment of the group, comprising the illustration, to another group or atom. The term "solid support" (SS), as used in the present invention, signifies polymeric material for supported synthesis. Solid support should be acid labile, photochemically cleavable to facilitate formation of a compound of Formula I, and should be chemically stable under the conditions of the present process. Illustrative examples of SS are 3,5-dimethoxy-4-formylphenoxy polystyrene, 2-(3,5-dimethoxy-4-formylphenoxy)ethoxy- methyl polystyrene, 2-(3,5-dimethoxy-4- formylphenoxy)ethyl polystyrene, 4-(3,5-dimethoxy-4- formylphenoxy)butyramidomethyl polystyrene, 4-(3,5-dimethoxy-4- formylphenoxy)propionamidomethyl polystyrene, and 4-(3,5-dimethoxy-4- formylphenoxy)acetamidomethyl polystyrene (all collectively known as PALS). A detailed description of the terms linker molecule and solid support can be found in The Combinatorial Index, B. A. Bunin, Academic Press (1998), which is incorporated herein by reference.
The term "deprotecting agent" is used to mean an agent which selectively removes a PG from a functional group such as an amine group. The deprotecting agent can be an acidic or basic moiety as understood by one skilled in the art. The term "protecting group" or "PG", as used herein, indicates a group that protects an amine functional group rendering the amine inactive. A detailed description of the terms "deprotecting agent", and "protecting group" (PG) is available in Protective Groups in Organic Synthesis, 2nd edition, T. W. Greene and P. G. M. Wuts, 1991, which is incorporated herein by reference. "Suitable Solvent", as used herein is meant to indicate a solvent which is compatible with reducing conditions and able to swell the solid support (SS). Representative examples of suitable solvent are THF, dioxane, toluene, dimethyl formamide (DMF), dimethyl sulfoxide (DMSO), dimethyl acetamide (DMA), dichloro methane (DCM), N-methyl pyrrolidinone (NMP) or mixtures thereof. A list of suitable solvents can be found in Tet. Lett. 1998, 39, 8451-54, and is incorporated herein by reference.
"Alkyl", or "alkyl radical" is meant to indicate a saturated or partially unsaturated hydrocarbon moiety containing 1 to 14 carbon atoms. This hydrocarbon moiety is generally attached to at least one other atom, and can be straight chain, or branched, or cyclic. An example of a partially unsaturated hydrocarbon moiety is an "alkelene" group which has at least one center of unsaturation, i.e., a double bond. Illustrative examples are butene, butadiene, propene, and pentene. A cyclic hydrocarbon moiety is represented by "cycloalkyl", "cycloalkyl ring", or "cycloalkyl radical" which can be saturated or partially unsaturated three to ten carbon monocyclic or bicyclic hydrocarbon moiety which is optionally substituted with an R7 and R8 groups. The term straight chain alkyl is meant to represent an unbranched hydrocarbon moiety of up to 8 carbon atoms. An example of a straight chain alkyl is a n-pentyl group.
The term "aryl" means an aromatic monocyclic, bicyclic, or a fused polycyclic hydrocarbon radical containing the number of carbon atoms indicated. Thus a C6-C14 aryl group includes phenyl, naphthyl, anthracenyl, etc. The term "heteroaryl" means aryl, as defined above, wherein one or more of the carbon atoms is replaced by a hetero atom chosen from N, O, and S. The hetero atoms can exist in their chemically allowed oxidation states. Thus Sulfur (s) can exist as a sulfide, sulfoxide, or sulfone. Each heteroaryl ring comprises from five (5) to fourteen (14) atoms. Illustrative examples of heteroaryl groups are thienyl, furyl, pyrrolyl, indolyl, pyrimidinyl, isoxazolyl, purinyl, imidazolyl, pyridyl, pyrazolyl, quinolyl, and pyrazinyl.
The terms "hetero cyclic ring", "hetero cycloalkyl" and "hetero cycloalkyl ring" mean cycloalkyl, as defined above, except one or more of the carbon atoms of the cycloalkyl group are replaced by a hetero atom chosen from N, NR12, O , S(O), S(O)2 and S, wherein R12 is (C1 6)alkyl or hydrogen. Illustrative examples of the term hetero cycloalkyl are morpholinyl, indolinyl, piperidyl, pyrrolidinyl, pyrrolinyl, imidazolidinyl, quinuclidinyl and morpholinyl.
The term "amino acid" as used herein represents a natural or unnatural amino acid. The term "natural amino acid", as used herein is intended to represent the twenty naturally occurring amino acids in their L' form, which are some times also referred as 'common amino acids', a list of which can be found in Biochemistry, Harper & Row Publishers, Inc. (1983). The term "unnatural amino acid", as used herein, is intended to represent the 'D' or 'DL' forms of the twenty naturally occurring amino acids described above. It is further understood that the term unnatural amino acid includes homologues of the natural amino acids, and synthetically modified form of the natural amino acids. The synthetically modified forms include amino acids having alkylene chains shortened or lengthened by up to two carbon atoms, amino acids comprising optionally substituted aryl groups, and amino acids having halogenated groups, preferably halogenated alkyl and aryl groups. Additional description of the term "amino acid" can be found in US Patent Numbers 5,514,694 and 5, 610,297, and BaChem Chemicals Catalog (1999) which are all incorporated herein by reference.
The term "natural amino acid side chain" is intended to represent a natural amino acid ("natural amino acid" as defined above) wherein a keto (C=O) group replaces the carboxylic acid group in the amino acid. Thus, for example, an alanine side chain is C(=O)-CH(NH2)-CH3; a valine side chain is C(=O)-CH(NH2)-CH(CH3)2; and a cysteine side chain is C(=O)-CH(NH2)-CH2-SH. The term "unnatural amino acid side chain" is intended to represent an unnatural amino acid ("unnatural amino acid" as defined above) wherein a keto (C=O) group replaces the carboxylic acid group forming unnatural amino acid side chains similar to ones illustrated under the definition of "natural amino acid side chain" above.
It thus follows that a "N-natural amino acid side chain" substituent and "N- unnatural amino acid side chain" substituent is a group wherein the nitrogen atom (N) is the annular ring atom substituted with a natural or unnatural amino acid side chain (natural or unnatural amino acid side chain is a defined above). The point of attachment between the nitrogen atom and the natural or unnatural amino acid side chain is at the keto (C=O) group of the respective amino acids. Thus a N-natural amino acid, i.e., N-cysteine, is N-C(=O)-CH(NH2)-CH2-SH.
The term "protected natural amino acid" represents an amino acid, as defined above, wherein the amino group and/or the side chain of the amino acid is protected with an amino acid protecting group. The term "protected unnatural amino acid" represents an unnatural amino acid, as defined earlier, wherein the amine group of the unnatural amino acid or its side chain is protected with an amino acid protecting group. The term "varied structural order" as used herein is intended to explain the structural arrangement of the peptide or peptidal derivatives represented by, for example, Formula II in the present invention. Thus a compound or compounds of Formula II which comprise amino acid components can have these amino acid components arranged in any order such that the compounds of Formula II have a diverse or varied structural order thereby making these compounds distinct from one another. "Optional substituents" for aryl, hetero aryl, and Ph groups are R7 and R8. These R7 substituents at each occurrence are independently selected from a group consisting of H, NH,, halo, O-C alkyl, NHC,-C4 alkyl, N(C,-C4)2 alkyl, and CF3; while R8 is selected from H and CM alkyl.
List of abbreviations:
Ac: acetyl
AcOH: acetic acid Ac2O: acetic anhydride
ACN: acetonitrile
AMC: 7-amino-4-methylcoumarin
BH3.pyridine : borane pyridine complex
BHj.dimethylsulfide: borane dimethyl sulfide complex BHj.THF: borane tetrahydrofuran complex
Boc: t-butyloxycarbonyl
Bu4NOH: tetrabutylammonium hydroxide
CBZ: benzyloxycarbonyl
DCM: dichloromethane DIC: diisopropylcarbodiimide
DIPCDI: diisopropylcarbodiimide
DIPEA: diisopropylethylamine
DMA: N,N-dimethyl formamide
DMAP: 4-N,N-dimethylaminopyridine DMF: dimethylformamide
DMSO: dimethylsulfoxide
Fmoc: 9-fluorenylmethyloxycarbonyl
HATU: O-(7-azabenzotriazo- 1 -yl)- 1,1,3 ,3-tetramethyluronium hexafluorophosphate
HO Ac: acetic acid HOBt: hydroxybenzotriazole
IBC: isobutylchloroformate KOTMS: potassium trimethylsilyloxide LAMPS: large scale multiple peptide synthesizer MeOH: methanol
NaBH(OAc)3: sodium triacetoxyborohydride PIP: piperidine
NMM: N-methyl morpholine Orn: Ornithine
POCl3: phosphorous oxychloride TES: triethyl silane TFA: trifluoroacetic acid THF: tetrahydrofuran TMSC1: chlorotrimethylsilane wrt: with respect to

Claims

1. A process for synthesizing a compound or an array of compounds of Formula
I:
Figure imgf000030_0001
Formula I
wherein: R1 represents a protected or unprotected natural or unnatural amino acid side chain;
R2 represents a protected or unprotected natural or unnatural amino acid side chain;
R3 represents H or C -alkyl; alternatively
R2 and R3 along with the carbon and nitrogen atom to which they are attached form a five to ten membered hetero cyclic ring; R4 represents R a or H;
R4a represents R5, SO2-R10 , CO-OR10, C(O)-NH-R10, C(S)-NH-R10, C(O)-R10 or C(S)-
R10;
L represents a fluorescent moiety;
SS represents a solid support; R5 represents an amino acid protecting group; and
R10 represents H, aryl, (CEL,).^ aryl, (CH,)06 heteroaryl, C,_8 alkyl, C4 14 branched alkyl or C4_I4 cycloalkyl; the process comprising the steps of
(i) reacting, in a suitable solvent, a primary amine of Formula-1
Figure imgf000031_0001
.Formula-1,
with either:
(a) a compound of Formula-2A
SS-CHO .Formula-2A,
in the presence of a reducing agent, or
(b) a compound of Formula-2B,
SS-CH.-X .Formula-2B,
to form a secondary amine of Formula 3
Figure imgf000031_0002
.Formula-3,
where L, SS and R' are as defined above and X is a leaving group;
(ii) treating the secondary amine of Formula-3, with a compound of Formula-4
Figure imgf000031_0003
.Formula-4, to form a compound of Formula-I, where R4 represents R4a, and
R2, R3 and R4a are as defined above, to form a compound of Formula I; and
(iii) optionally treating a compound of Formula I, where R4a represents R5, with a deprotecting agent to form a compound of Formula I, where R4 represents H.
2. A process for synthesizing a compound or an array of compounds of Formula II
Figure imgf000032_0001
Formula II wherein:
R1 represents a protected or unprotected natural or unnatural amino acid side chain; R2 independently at each occurance represents a protected or unprotected natural or unnatural amino acid side chain;
R3 independently at each occurance represents H or C1 4-alkyl; alternatively
R2 and R3 independently at each occurance along with the carbon and nitrogen atom to which they are attached form a five to ten membered hetero cyclic ring; R4 represents R a or H;
R4a represents R5, SO2-R10 , CO-OR10, C(O)-NH-R10, C(S)-NH-R10, C(O)-R10 or C(S)-
R10;
L represents a fluorescent moiety;
R5 represents an amino acid protecting group; R10 represents H, aryl, (CFL,),^ aryl, (Cli,)^ heteroaryl, C,.8 alkyl, C4.14 branched alkyl or C4.14 cycloalkyl; and
"n" represents an integer from 1 to 7; said process comprising
(a) treating a compound of Formula-5
Figure imgf000033_0001
.Formula-5
where R1, R2 and R3 are as defined above, SS represents a solid support, and "q" represents an integer from about 0 to 6, with a compound of Formula-4
Figure imgf000033_0002
.Formula-4
where R2, R3 and R4a are as defined above, to form a compound of Formula-6
Figure imgf000033_0003
.Formula-6
where R1, R2, R3, R4a, SS, "n" and L are as defined above;
(b) optionally treating a compound of Formula-6, when R4J = R5, with a deprotecting agent to form a compound of Formula-9
Figure imgf000034_0001
.Formula-9
where R1, R2, R3, SS, "n" and L are as defined above; and
(c) treating a compound of Formula-6 or a compound of Formula-9 with a strong acid to yield a compound of Formula II.
3. A process of Claim 1 wherein
L represents a fluorescent moiety selected from 4-methyl-2-oxo-2H-chromen-7- ylamino, 2-oxo-4-trifluoromethyl-2H-chromen-7-ylamino, 4- methoxycarbonylmethyl-2-oxo-2H-chromen-7-ylamino, 2-oxo-4-(2-oxo-ethyl)-2H- chromen-7-ylamino, 2-oxo-2H-chromen-7-ylamino, 4-nitro-phenylamino, 5- dimethylsulfamoyl-naphthalen-1 -ylamino, naphthalen-1 -ylamino, 5-methoxy- naphthalen-l -ylamino, and rhodamino; and SS represents a solid support selected from PALS.
4. A process of Claim 3 wherein the reducing agent in step (i)(a) is selected from NaBH(OAc)3, diborane, B^.pyridine, BH3.dimethylsulfide, BH3.THF, NaBH4, NaCNBH3, Zn(BH4)2 and LiBH4.
5. A process of Claim 4 wherein L represents 4-methyl-2-oxo-2H-chromen-6- ylamino.
6. A process of Claim 2 wherein L represents a fluorescent moiety selected from 4-methyl-2-oxo-2H-chromen-7- ylamino, 2-oxo-4-trifluoromethyl-2H-chromen-7-ylamino, 4- methoxycarbonylmethyl-2-oxo-2H-chromen-7-ylamino, 2-oxo-4-(2-oxo-ethyl)-2H- chromen-7-ylamino, 2-oxo-2H-chromen-7-ylamino, 4-nitro-phenylamino, 5- dimethylsulfamoyl-naphthalen-1 -ylamino, naphthalen-1 -ylamino, 5-methoxy- naphthalen-l -ylamino, and rhodamino; and "n" represents an integer from 0 to 5.
7. A process of Claim 6 wherein L represents 4-methyl-2-oxo-2H-chromen-6- ylamino.
8. A compound of Formula-3
Figure imgf000035_0001
Formula-3,
wherein:
R1 represents a protected or unprotected natural or unnatural amino acid side chain; L represents a fluorescent moiety; and SS represents a solid support.
9. A compound of Claim 8 wherein
L represents a fluorescent moiety selected from 4-methyl-2-oxo-2H-chromen-7- ylamino, 2-oxo-4-trifluoromethyl-2H-chromen-7-ylamino, 4- methoxycarbonylmethyl-2-oxo-2H-chromen-7-ylamino, 2-oxo-4-(2-oxo-ethyl)-2H- chromen-7-ylamino, 2-oxo-2H-chromen-7-ylamino, 4-nitro-phenylamino, 5- dimethylsulfamoyl-naphthalen-1 -ylamino, naphthalen-1 -ylamino, 5-methoxy- naphthalen-l -ylamino, and rhodamino.
10. A process for the synthesis of a compound or an array of compounds of Formula-6
Figure imgf000036_0001
.Formula-6
wherein
R! represents a protected or unprotected natural or unnatural amino acid side chain;
R2 independently at each occurance represent a protected or unprotected natural or unnatural amino acid side chain;
R3 independently at each occurance represents H or C -alkyl; alternatively
R2 and R3 independently at each occurance along with the carbon and nitrogen atom to which they are attached form a five to ten membered hetero cyclic ring;
R4 represents R4a or H;
R4a represents R5, SO2-R10 , CO-OR10, C(O)-NH-R10, C(S)-NH-R10, C(O)-R'° or C(S)-
R10;
L represents a fluorescent moiety;
SS represents a solid support;
R5 represents an amino acid protecting group;
R10 represents H, aryl, (CFL,),,^ heteroaryl, (CLL,),^ aryl, C,.8 alkyl, C4.14 branched alkyl, or C4 14 cycloalkyl; and
"n" represents an integer from 1 to 7; the process comprising treating a compound of Formula A
Figure imgf000036_0002
.Formula A
with a compound of Formula B
Figure imgf000037_0001
.Formula B
where R , R , R , R \ L and SS are as defined above, and "v" represents an integer of from 1 to 5, to form a compound of Formula-6.
11. A process for synthesizing a compound or an array of compounds Formula II
Figure imgf000037_0002
Formula II wherein:
R1 represents a protected or unprotected natural or unnatural amino acid side chain;
R2 independently at each occurance represents a protected or unprotected natural or unnatural amino acid side chain;
R3 independently at each occurance represents H or C,.4-alkyl; alternatively R2 and R3 independently at each occurance along with the carbon and nitrogen atom to which they are attached form a five to ten membered hetero cyclic ring;
R4 represents R4a or H;
R4a represents R5, SO2-R10 , CO-OR10, C(O)-NH-R10, C(S)-NH-R10, C(O)-R'° or C(S)-
R10; L represents a fluorescent moiety;
R5 represents an amino acid protecting group;
R10 represents H, aryl, (CFL,),^ aryl, (CH ^ heteroaryl, C,.8 alkyl, .^ branched alkyl or C^u cycloalkyl; and "n" represents an integer from 1 to 7; said process comprising
(a) treating a compound of Formula-6 when R4a = R5,
Figure imgf000038_0001
.Formula-6
with a deprotecting agent to form a compound of Formula-9
Figure imgf000038_0002
.Formula-9
where R1, R2, R3, SS, "n" and L are as defined above;
(b) treating a compound of Formula-9 with a compound of Formula-12
R4a-X .Formula-12
where R4a is as defined above, to form a compound of Formula-6; and
(c) treating a compound of Formula-6 or a compound of Formula-9 with a strong acid to yield a compound of Formula II.
PCT/US2000/021710 1999-08-10 2000-08-08 Process of synthesis of fluorescent protease substrates WO2001010890A2 (en)

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