AU713492B2

AU713492B2 - Reversible protease inhibitors

Info

Publication number: AU713492B2
Application number: AU53674/96A
Authority: AU
Inventors: Jeffrey L. Klaus; James T. Palmer; David Rasnick
Original assignee: Axys Pharmaceuticals Inc
Current assignee: Axys Pharmaceuticals Inc
Priority date: 1995-03-24
Filing date: 1996-03-21
Publication date: 1999-12-02
Anticipated expiration: 2016-03-21
Also published as: AU5367496A; KR19980703261A; CA2216151A1; WO1996030353A1; CN1184472A; TW470750B; NO311573B1; NO974403L; JPH11503417A; MY113489A; NO974403D0; CN1071751C; EP0817778A1; CZ298197A3; PL322409A1; ZA962336B; NZ305626A; IL117638A0

Description

WO 96/30353 PCTI/US96/03844 1 REVERSIBLE PROTEASE INHIBITORS FIELD OF THE INVENTION The invention relates to novel reversible protease inhibitors. The inhibitors are selective for cysteine proteases.

BACKGROUND OF THE INVENTION Cysteine or thiol proteases contain a cysteine residue at the active site responsible for proteolysis.

Since cysteine proteases have been implicated in a number of diseases, including arthritis, muscular dystrophy, inflammation, tumor invasion, glomerulonephritis, malaria, and other parasite-borne infections, methods for selectively and irreversibly inactivating them provide opportunities for new drug candidates. See, for example, Esser, R.E. etal., Arthritis Rheumatism (1994) 37, 236; Meijers, M.H.M. et al., Agents Actions (1993), 39 (Special Conference Issue), C219; Machleidt, W. et al, Fibrinolysis (1992), 6 Suppl. 4, 125; Sloane, B.F. et al., Biomed. Biochim. Acta (1991), 50, 549; Duffy, Clin. Exp. Metastasis (1992), 10, 145; Rosenthal, Wollish, Palmer, Rasnick, D., J. Clin. Investigations (1991), 88, 1467; Baricos, W.H. et al, Arch. Biochem. Biophys. (1991), 288, 468; Thornberry, N.A. et al., Nature (1992), 356, 768.

Low molecular weight inhibitors of cysteine proteases have been described by Rich, Proteinase Inhibitors (Chapter 4, "Inhibitors of Cysteine Proteinases"), Elsevier Science Publishers (1986). Such inhibitors include peptide aldehydes, which form hemithioacetals with the cysteine of the protease active site. See, for instance, Cheng, Keitz, and Jones, J. Org. Chem. (1994), 59, 7671.

The disadvantage of aldehydes is their in vivo and chemical instabilities.

Aldehydes have been transformed into a,B1-unsaturated esters and sulfones by means of the Wadsworth-Emmons-Horner modification of the Wittig reaction, shown below (Wadsworth, W.S. and WO 96/30353 PCT/US96/03844 2 Emmons, W.D. Am. Chem. Soc. (1961), 83, 1733).

0 o EtO--PW EWG baseEWG R+D IE R H EtO where R alkyl, aryl, etc.

EWG COOEt, SO 2 Me, etc.

a,ll-unsaturated esters (Hanzlik et al., J. Med. Chem., 27(6):711-712 (1984), Thompson et al., J. Med.

Chem. 29:104-111 (1986), Liu et al., J. Med. Chem., 35(6):1067 (1992)) and a, l-unsaturated sulfones (Thompson et al., supra, Liu et al., supra) were tested as inhibitors of two cysteine proteases, papain and dipeptidyl amino-peptidase I (also called cathepsin However, the inhibition of papain by these a,l-unsaturated compounds showed poor inhibition, evidenced by second order rate constants from less than 1 M'sec- 1 to less than 70 M-'sec- 1 for the a,l-unsaturated esters, and from less than 20 M 'sec' to less than 60 M-'sec' 1 for the sulfone.

In addition, this chemistry has not been demonstrated with derivatives of a-amino acids other than those corresponding to glycine, or in the case of the ester, phenylalanine. Thus the chirality of these compounds is non-existent for the glycine derivatives and unclear for the phenylalanine derivatives.

This is significant since inhibition of an enzyme generally requires a chiral compound.

Alpha-amino sulphonic acids were suggested as potential inhibitory compounds, and several were made, although their inhibitory effects were not reported (Mcllwain et al., J. Chem. Soc. 75 (1941)).

In addition, the Mannich condensation of sulfinic acid, aldehyde, and ethyl carbamate, to form urethanes has been reported (Engberts et al., Recueil 84:942 (1965).

Additional methods for selectively and irreversibly inhibiting cysteine proteases have relied upon alkylation by peptide a-fluoromethyl ketones (Rasnick, Anal. Biochem. (1985), 149, 416), diazomethyl-ketones (Kirschke, Shaw, E. Biochem. Biphys. Res. Commun. (1981), 101, 454), acyloxymethyl ketones (Krantz, A. et al., Biochemistry, (1991), 30, 4678; Krantz, A. et al., U.S. Patent 5,055,451, issued October 8, 1991), and ketosulfonium salts (Walker, Shaw, Fed. Proc. Fed.

Am. Soc. Exp. Biol., (1985), 44, 1433).

Other families of cysteine protease inhibitors include epoxysuccinyl peptides, including E-64 and its analogs (Hanada, K. et al., Agric. Biol. Chem (1978), 42, 523; Sumiya, S. et Chem. Pharm. Bull.

((1992), 40, 299 Gour-Salin, B.J. et al., J. Med. Chem., (1993), 36, 720), a-dicarbonyl compounds, WO 96/30353 PCTIUS96/03844 3 reviewed by Mehdi, Bioorganic Chemistry, (1993), 21, 249, and N-peptidyl-O-acyl hydroxamates (Bromme, Neumann, Kirschke, Demuth, Biochim. Biophys. Acta, (1993), 1202, 271.

An additional summary of methods for reversibly and irreversibly inhibiting cysteine proteases has recently been compiled; see Shaw, Advances in Enzymology and Related Areas of Molecular Biology (1990), 63, 271.

SUMMARY OF THE INVENTION An aspect of this invention is a protease inhibitor comprising a targeting group linked through a two carbon atom chain to an electron withdrawing group, wherein the dissociation constant for inhibition of the protease with said inhibitor is no greater than about 100 pM.

An additional aspect of this invention is a protease inhibitor comprising a targeting group linked either directly or through a linker selected from the group consisting of an intermediate carbon atom or a two carbon atom chain to a sulfone group group, wherein the dissociation constant for inhibition of the protease with said inhibitor is no greater than about 100 pM.

A further aspect of this invention is a compound, preferably a protease inhibitor, of Formula I: R Z B Z A Z X S(O)R 2 in which: n is 0 to 13; A-B represents a linkage selected from -C(O)NR 3

-CH

2

NR

3

-C(O)CH

2 and -NR 3 wherein R 3 is hydrogen or as defined below; X represents a bond, methylene or the linkage -CH 2

CH(R

4 wherein R 4 is hydrogen, alkyl or arylalkyl; Y is -CH(R 5 or -NR 5 wherein R 5 is hydrogen or as defined below; Z is -(CH 2 2

-C(R

6

)(R

7 or -N(R 7 wherein R 6 is hydrogen or methyl and R 7 is as defined below; Z' is -(CH 2 2

-C(R

6 or -N(R 8 wherein R 6 is hydrogen or methyl and R 8 is as defined below; R' is hydrogen, alkyloxycarbonylalkanoyl, alkyloxycarbonyl, alkanoyl (optionally substituted with a radical selected from carboxy, alkyloxycarbonyl and heterocycloalkylalkanoylamino), cycloalkylcarbonyl, heterocycloalkylcarbonyl (optionally substituted with a radical selected from hydroxy, alkyl, alkanoyl, alkyloxycarbonyl, arylalkyloxycarbonyl and heterocycloalkylcarbonyl), arylalkyloxycarbonyl, carbamoyl, alkylcarbamoyl, dialkylcarbamoyl, arylcarbamoyl, arylalkylcarbamoyl, arylalkanoyl, aroyl, alkylsulfonyl, dialkylaminosulfonyl, arylsulfonyl or heteroarylsulfonyl;

R

7 and R 8 are independently hydrogen, alkyl (optionally substituted with a radical selected from hydroxy, amino, alkylamino, dialkylamino, uriedo, mercapto, alkylthio, carboxy, carbamoyl, WO 96/30353 PCT/US96/03844 4 alkylcarbamoyl, dialkylcarbamoyl, alkylsulfonyl and guanidino, or a protected derivative thereof), cycloalkyl, cycloalkylalkyl, heteroaryl, heteroarylalkyl, a group selected from aryl and arylalkyl (which group is optionally substituted at its aryl ring with one to three radicals selected from hydroxy, amino, guanidino, halo, optionally halo-substituted alkyl, alkyloxy and aryl, or a protected derivative thereof) or together with an adjacent R 3 or R 5 forms a divalent radical selected from (C3-)methylene and 1,2-phenylenedimethylene (which radical is optionally substituted with hydroxy, or a protected derivative thereof, or oxo); and

R

2 is hydrogen, alkyl (optionally substituted with one or more radicals selected from amino, guanidino, halo, hydroxy, alkyloxy, nitro, alkylsulfonyl and arylsulfonyl, or a protected derivative thereof), cycloalkyl, cycloalkylalkyl or a group selected from aryl and arylalkyl (which group is optionally substituted at its aryl ring with one to two radicals selected from amino, halo, hydroxy, optionally halo-substituted alkyl, alkyloxy, nitro, alkylsulfonyl and arylsulfonyl, or a protected derivative thereof); and the pharmaceutically acceptable salts, individual isomers and mixtures of isomers thereof, preferably wherein the dissociation constant for inhibition of the protease with said inhibitor is no greater than about 100 pM.

An additional aspect of this invention is a compound, preferably a protease inhibitor, of Formula II: RI/ Y A B Z 'A B Z R 9 in which: the groups are as defined above and

R

9 is cyano, -C(O)OR'O, -P(O)(ORO) -S(O)(NR)Ro 0

C(O)R

1 1

-C(O)NR

2

R

1 3

-S(O)

2

NR

2

R

13

-C(O)NHR

1 4 or -S(O) 2

NHR

1 4 wherein each R 1 0 is independently hydrogen, alkyl (optionally substituted with one or more radicals selected from amino, halo, hydroxy, alkyloxy, nitro, alkylsulfonyl and arylsulfonyl, or a protected derivative thereof), cycloalkyl, cycloalkylalkyl or a group selected from aryl and arylalkyl (which group is optionally substituted at its aryl ring with one to two radicals selected from amino, halo, hydroxy, optionally halo-substituted alkyl, alkyloxy, nitro, alkylsulfonyl and arylsulfonyl, or a protected derivative thereof), R" is hydrogen, alkyl, perfluoroalkyl, cycloalkyl, cycloalkylalkyl, perfluoroaryl, perfluoroarylakyl or a group selected from aryl and arylalkyl (which group is optionally substituted at its aryl ring with one to two radicals selected from amino, halo, hydroxy, optionally halo-substituted alkyl, alkyloxy, nitro, alkylsulfonyl and arylsulfonyl, or a protected derivative thereof), R 12 and R 3 are independently hydrogen, alkyl, cycloalkyl, cycloalkylalkyl, aryl or aralkyl, and R 14 is -C(O)OR' 1 in which Ro 1 is as defined above, or a group selected from Formulae and 0 Z A B A B Z OR 'o Z A R o 0 (b) wherein each n, A, B, Y, Z, R' and R' 1 are as defined above, and the pharmaceutically acceptable salts; individual isomers and mixtures of isomers thereof, preferably wherein the dissociation constant for inhibition of the protease with said inhibitor is no greater than about 100 pM.

A further aspect of this invention is a compound, preferably a protease inhibitor, of Formula II1: D, /Y Z,7 A Z B

R"

1 116

R

III

in which: the groups are as defined above and R'S is hydrogen, methyl, fluoro or a group selected from Formulae and as defined above, and

R

16 is a group selected from phenyl or (Cs)heteroaryl (which group is optionally substituted with at least one radical selected from alkylcarbamoyl, dialkylcarbamoyl, alkyloxycarbonyl, alkylsulfinamoyl, dialkylsulfinamoyl, alkylsulfonyl, carboxy, nitro, sulfinamoyl, sulfo, carbamoyl, phosphono, alkyloxyphosphinyl, dialkyloxyphosphinyl, alkanoyl, cyano, alkylsulfinyl, sulfamoyl, alkylsulfamoyl, dialkylsulfamoyl, alkyloxysulfonyl, alkylsulfonimidoyl, aryl, heteroaryl, hydroxy, alkyloxy, optionally halo-substituted alkyl, arylalkyl, halo, -+N(R 7 3 wherein each R 7 is independently alkyl, aryl or arylalkyl, or

-N(R

8 2 wherein each R 8 is independently hydrogen, alkyl, aryl or arylalkyl); and the pharmaceutically acceptable i salts; individual isomers and mixtures of isomers thereof, preferably wherein the dissociation constant for inhibition of the protease with said inhibitor is no greater than about 100M.

An additional aspect of this invention is a pharmaceutical composition comprising a therapeutically effective amount of a cysteine protease inhibitor of the invention, or of an individual isomer, a mixture of isomers, or the pharmaceutically acceptable salt or salts thereof, in combination with one or more pharmaceutically acceptable excipients.

A further aspect of this invention is a method for treating a condition capable of amelioration by inhibition of a cysteine protease in an animal in need thereof, which method comprises administering to such animal a therapeutically effective amount of a cysteine protease inhibitor of the invention, or of San individual isomer, mixture of isomer, or the pharmaceutically acceptable salt or salts thereof.

WO 96/30353 PCT/US96/03844 6 Another aspect of this invention is a method for detecting a cysteine protease in a sample, which method comprises: assaying said sample for protease activity using a protease substrate: assaying for protease activity in the presence of a known concentration of cysteine protease inhibitor on the invention; and calculating the difference between a) and b) to determine the protease activity due to cysteine protease.

An aspect of this invention are the processes for preparing the cysteine protease inhibitors of this invention.

BRIEF DESCRIPTION OF THE DRAWINGS Figure 1 depicts Scheme I, the synthesis of Formula I compounds when X is a bond. The synthetic steps are as follows: a) HCO 2 H, H 2 0; b) HBr/acetic acid; c) 4-methylmorpholine, isobutyl chloroformate, Mu-ROH; and d) chromatographic purification. The groups are as defined herein.

Figure 2 depicts Scheme 2, the synthesis of Formula I compounds when X is a methylene group. The synthetic steps are as follows: a) 4-methylmorpholine, isobutyl chloroformate, followed by NaBH, reduction in water/THF; b) CH 3

SO

2 CI, triethylamine, CH 2

CI

2 c) R,SH, NaH, CH 3 OH, THF, heat; d) 4-chloroperbenzoic acid, CH 2

CI

2 e) HCI/dioxane or p-CH 3

C

6

H

4

SO

3 H/ether; and f) Mu-ROH, 4methylmorpholine, isobutyl chloroformate.

Figure 3 depicts Scheme 3, the synthesis of Formula I compounds when X is a methylene group. The synthetic steps are as follows: a) (CH 3 3

CH

2

CH

2 SH, NaH, MeOH, THF, heat; b) 4-chloroperbenzoic acid; c) (n-C 4

H,)

4 THF, followed by BrCH 2 CI, heat; d) HCI/dioxane or 4-CH 3

C

6

H

4

SO

3 H/ether, and; e) 4-methylmorpholine, isobutyl chloroformate, Mu-PheOH.

Figure 4 depicts Scheme 4, the synthesis of Formula II compounds. The synthetic steps are as follows: a) CI'H 2 N (CH 3

)OCH

3 dicyclohexylcarboiimide, Et 3

N/CH

2

CI

2 b) LiAIH4/THF; c) NaH/THF; d) Hcl/dioxane/CH 2

CI

2 e) 4-methylmorpholine, isobutyl chloroformate/THF; and f) H 2 5% Pd/C.

Figure 5 depicts Scheme 5, the synthesis of Formula 1 compounds when X is an ethylene. The synthetic steps are as follows: a)(CH20)n, HCI, dioxane, for instance where Ar 2-naphthyl; b) (EtO) 3 P; c) CH 3

CO

3 H, CH 2

CI

2 d) NaH, THF; e) p-CH 3

C

6

H

4

SO

3 H, Et 2 O; f) 4-methylmorpholine, isobutyl chloroformate; and g) H 2 Pd/C.

Figure 6 depicts the synthesis of compounds of Formula II in which R 9 is -COOH.

WO 96/30353 PCTIUS96/03844 7 Figure 7 depicts the synthesis of compounds of Formula II in which R 9 is -P(O)(R 10 2 The synthetic scheme is as follows: a) NaHITHF; b) anhydrous p-CH 3

C

6

H

4

SO

3 H/ether; c) 4-methylmorpholine, isobutyl chloroformate/THF, and; d) H 2 Pd/C.

Figure 8 depicts the synthesis of compounds of Formula II in which R 9 is -C(O)NHR' 4 The synthetic scheme is as follows: a) NaOH/EtOH, followed by Hcl/H 2 0; b) benzylamine, dicyclohexylcarbodiimide,

CH

2

CI

2 c) NaH/THF, diethyl benzylamidomethylenephosphonate; d) HCI/dioxane; e) 4-methylmorpholine, isobutyl chloroformate, THF; f) H 2 Pd/C, and as an alternative preparation from carboxylates as synthesized via Scheme 6, above; and g) aniline, dicyclohexylcarbodiimide, CHCI2- Figure 9 depicts the general synthesis of compounds of Formula II.

Fiaure 10 dpnirts the svnthesis of cnmnninds of Formild III The svnthtir stPne are ns fni!ws a

CH

3 CN or other suitable solvent, reflux; b) H 2 0, NaOH, followed by extraction into organic medium; c) phosphorane, THF (Wittig reaction); d) p-CH 3

C

6

HSO

3 H, ether; e) Mu-PheOH, 4-methylmorpholine, isobutyl chloroformate, THF; and f) H 2 Pd/C.

DEFINITIONS

Unless otherwise stated, the following terms used in the specification and claims are defined for the purposes of this application and have the meanings given below: "Alkyl", as in alkyl, alkyloxy, alkylthio, alkylsulfonyl, alkylcarbamoyl, dialkylcarbamoyl, heteroarylalkyl, arylalkyl, and the like, means a straight or branched, saturated or unsaturated hydrocarbon radical having from 1 to 10 carbon atoms or the number of carbon atoms indicated methyl, ethyl, propyl, isopropyl, butyl, sec-butyl, isobutyl, tert-butyl, vinyl, allyl, 1-propenyl, isopropenyl, 1-butenyl, 2-butenyl, 3-butenyl, 2-methylallyl, ethynyl, 1-propynyl, 2-propynyl, etc.).

"Alkyloxyphosphinyl" and "dialkyloxyphosphinyl" mean the radicals -P(O)(OH)OR and -P(O)(OR) 2 respectively, wherein R is alkyl as defined above.

"Alkanoyl", as in alkanoyl, alkanoyloxy, heterocycloalkylalkanoylamino, and the like, means the radical wherein R is alkyl as defined above, having overall from 1 to 11 carbon atoms or the number of carbon atoms indicated (C 1 ,,)alkanoyl includes the radicals formyl, acetyl, propionyl, isopropionyl, butyryl, isobutyryl, crotonoyl, isocrotonyl, etc.).

"Aryl" means an aromatic monocyclic or polycyclic hydrocarbon radical containing 6 to 14 carbon WO 96/30353 PCT/US96/03844 8 atoms or the number of carbon atoms indicated and any carbocylic ketone or thioketone derivative thereof, wherein the carbon atom with the free valence is a member of an aromatic ring, aryl includes phenyl, naphthyl, anthracenyl, phenanthrenyl, 1,2,3,4-tetrahydro-5-naphthyl, 1-oxo-1,2-dihydro-5-naphthyl, 1-thioxo-1,2-dihydro-5-naphthyl, etc.).

"Aroyl" means the radical -C(O)Ar, wherein Ar is aryl as defined above, having overall from 7 to carbon atoms or the number of carbon atoms indicated (C 7 1 ,)aroyl includes benzoyl, naphthoyl, etc.).

"Cycloalkyl", as in cycloalkyl and cycloalkylalkyl, means a saturated or unsaturated, monocyclic or polycyclic hydrocarbon radical containing 3 to 20 carbon atoms or the number of carbon atoms indicated, wherein the carbon atom with the free valence is a member of a non-aromatic ring, and any carbhocvclir. ketone and thioketone derivative thereof the term cycloalkyl is meant to include cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, cyclohexenyl, bicyclo[2.2.2]octyl, 1,2,3,4-tetrahydro- 1-naphthyl, oxocyclohexyl, dioxocyclohexyl, thiocyclohexyl, 9-fluorenyl, etc.).

"Halo" means fluoro, chloro, bromo or iodo.

"Heterocycloalkyl", as in heterocycloalkyl, heterocycloalkylalkanoylamino, heterocycloalkylcarbonyl, heterocycloalkylcarbonyl, and the like, means cycloalkyl as defined above wherein 1 to 5 of the indicated carbon atoms is replaced by a heteroatom chosen from N, O, S, P or As, wherein the atom with the free valence is a member of a non-aromatic ring, and any heterocyclic ketone, thioketone, sulfone or sulfoxide derivative thereof, the term heterocycloalkyl is meant to include piperidyl, pyrrolidinyl, pyrrolinyl, imidazolidinyl, indolinyl, quinuclidinyl, morpholinyl, piperazinyl, N-methylpiperazinyl, piperadinyl, 4,4-dioxo-4-thiapiperidinyl, 1,2,3,4-tetrahydro-3-isoquinolyl, 2,4-diaza-3-oxo-7-thia-6-bicyclo[3.3.0]octyl, etc.). Thus, hetero(C)cycloalkyl includes the radicals morpholinyl, piperazinyl, piperidinyl and the like.

"Heteroaryl" means an aromatic monocyclic or polycyclic hydrocarbon radical containing overall from to 14 atoms or the number of atoms indicated, wherein 1 to 5 of the indicated carbon atoms are replaced by a heteroatom chosen from N, O, S, P or As, wherein the atom with the free valence is a member of an aromatic ring, and any heterocyclic ketone and thioketone derivative thereof the term heteroaryl is meant to include thienyl, furyl, pyrrolyl, pyrimidinyl, isoxazolyl, oxaxolyl, indolyl, benzo[b]thienyl, isobenzofuranyl, purinyl, isoquinolyl, pterdinyl, pyrimidinyl, imidazolyl, pyridyl, pyrazolyl, pyrazinyl, 4-oxo-1,2-dihydro-1 -naphthyl, 4-thioxo-1,2-dihydro-1-naphthyl, etc.). Thus, hetero(C 6 )aryl includes the radicals pyridyl, pyrimidinyl, and the like.

WO 96/30353 PCT/US96/03844 9 "1,2-Phenylenedimethylene" means a divalent radical of the formula -CH 2

C

6

H

4

CH

2 For example, the group R'Y-Z-A- in which Y is -N(R 5 Z is -CH(R 7 A is carbonyl and R 7 together with R 5 forms 1,2-diphenylenedimethylene" means a group of following formula:

R

and substituted derivatives and individual stereoisomers and mixture of stereoisomers thereof.

Substituted derivatives of the 1,2-phenylenedimethylene divalent radical may contain a hydroxy group on any carbon within the ring system or an oxo group on either of the unsaturated ring carbon atoms.

"Phosphono" means the radical 2 "Methylene" as in "(C 3 4)methylene"and "(C 37 )methylene" mean a straight, saturated divalent radical having the number of carbon atoms indicated; "(C 3 4 )methylene" includes trimethylene (-(CH 2 3 and tetramethylene (-(CH 2 4 For example, a preferred embodiment herein utilizes a proline residue as an A-B-Z group, wherein A-B represents CH 2

-NR

3 and R 3 together with either R 7 or R 8 form a C3 methylene. Thus, the group in which Y is -(NR 5 Z is -CH(R 7 A is carbonyl and R 7 together with R 5 forms trimethylene means a group of following formula: N -'Y R

O

and the individual stereoisomers and mixtures of stereoisomers thereof. Substituted derivatives of the trimethylene and tetramethylene divalent radicals may contain a hydroxy group, or a protected derivative thereof, or an oxo group on any of the ring carbon atoms. Suitable hydroxy protective groups are defined below.

"Oxa(C 37 )methylene" and "aza(C 37 )methylene" mean methylene as defined above wherein one of the indicated carbon atoms is replaced by an oxygen or nitrogen atom, respectively. For example, "oxa(C 5 )methylene" includes 3-oxapentamethylene (-CH 2

CH

2 0OCHCH 2 and 2-oxapentamethylene

(-CHOCHCH

2

CH

2 Thus, -C(O)NR 21

R

2 2 means the radical 4-morpholinylcarbonyl when R 21 and R 2 2 together form 3-oxapentamethylene and the radical 1-piperazinylcarbanoyl when R 21 and R 22 together form 3-azapentamethylene.

WO 96/30353 PCT/US96/03844 "Adjacent", as use in the phrase "R 7 together with an adjacent R 3 means that the atoms to which the

R

7 and R 3 groups are respectively attached are in turn attached to one another.

"Animal" includes humans, non-human mammals dogs, cats, rabbits, cattle, horses, sheep, goats, swine, deer, etc.) and non-mammals birds, etc.).

"Disease" specifically includes any unhealthy condition of an animal or part thereof and includes an unhealthy condition which may be caused by, or incident to, medical or veterinary therapy applied to that animal, the "side effects" of such therapy.

"Electron withdrawing group" (EWG) means a functional group that in its broadest sense is a group able to exert a polarizing force on the bond between itself and the carbon to which it is attached, such that ~letrons are polanzred in favor of the electron withdrawing group. While not being limited to any particular theory, it is believed that the polarizing property enables the electron withdrawing group to participate in hydrophobic or hydrogen bonding interactions with an active site of the cysteine protease, resulting in inhibition of the enzyme. In general, a moiety is suitable as an electron withdrawing group if when present in the a-position of a phosphonium ylide of the general structure Ph 3 P=C(R)EWG it exerts sufficient polarization to stablize the ylide against undergoing decomposition reactions with oxygen, water, hydrohalic acids, alcohols, and the like. Preferred electron withdrawing groups are those which would similarly stablilize ylides of the general formula (RO) 2

P(O)C(R)EWG.

Suitable electron withdrawing groups include cyano, -S(O) 2

-C(O)OR

1 0

-P(O)(OR

10 2 -S(O)(NR'o)R 10

C(O)R

1 1

-S(O)R

1 1

-C(O)NR

12

R'

3 2

NR

1 2

R

1 3 -C(O)NHR14, -S(0) 2

NHR

1 4 phenyl and (Cs 5 .)heteroaryl, wherein each R 2

R

1 0

R

11

R

12

R

1 3 and R 1 4 are as defined in their broadest definitions set forth in the Summary of the Invention. When the electron withdrawing group is phenyl or (C 5 .)heteroaryl the ring may be substituted with one or more meta directing groups alkyloxycarbonyl, alkylsulfinamoyl, dialkylsulfinamoyl, alkylsulfonyl, carboxy, nitro, sulfinamoyl, sulfo, phosphono, alkyloxyphosphinyl, dialkyloxyphosphinyl, alkanoyl, cyano, alkylsulfinyl, sulfamoyl, alkylsulfamoyl, dialkylsulfamoyl, alkyloxysulfonyl, disubstituted amino, trisubstituted ammonio, and the like), ortho and para directing groups hydroxy, alkyloxy, optionally halo-substituted alkyl, aryl, arylalkyl, halo, and the like) and electron withdrawing moieties alkylcarbamoyl, dialkylcarbamoyl, alkyloxycarbonyl, alkylsulfinamoyl, dialkylsulfinamoyl, alkylsulfonyl, carboxy, nitro, sulfinamoyl, sulfo, carbamoyl, phosphono, alkyloxyphosphinyl, dialkyloxyphosphinyl, alkanoyl, cyano, alkylsulfinyl, sulfamoyl, alkylsulfamoyl, dialkylsulfamoyl, alkyloxysulfonyl, aryl, heteroaryl, and the like).

"Leaving group" has the meaning conventionally associated with it in synthetic organic chemistry, i.e., an atom or group displaceable under alkylating conditions, and includes halo and alkane- or arenesulfonyloxy, sucha mesyloxy, ethanesulfonyloxy, benzenesulfonyloxy and tosyloxy, and WO 96/30353 PCT/US96/03844 11 alkaesulfonylamino, alkanecarbonylamino, aminosulfonylamino, aminocarbonylamino and the like.

Isomerism is the phenomenon wherein compounds have identical molecular formulae but differ in the nature or sequence of bonding of their atoms or in the arrangement of theri atoms in space. Isomers that differ in the arrangement of their atoms in space are termed "steroisomers". Stereoisomers that are not mirror images of one another are termed "diastereomers" and stereoisomers that are nonsuperimposable mirror images are termed "enantiomers" or sometimes "optical isomers". A carbon atom bonded to four nonidentical substituents is termed a "chiral center".

A compound with one chiral center has two enantiomeric forms of opposite chirality is termed a "racemic mixture". A compound that has more than one chiral center has 2 enantiomeric pairs, where n is the number of chiral centers. Compounds with more than one chiral center may exist as ether an individual diasteromer or as a mixture of diasterenmers, termr ed "diastereomeric mixture".

Compounds of Formulae I, II and III can exist as individual steroisomers or mixtures of stereoisomers.

For example, compounds of Formulae I, II and III contain a chiral center at the carbon to which the substituent R 8 is attached. Furthermore, compounds of Formulae I, II and III in which Z is -C(R 6

)(R

7 contain a chiral center at the carbon to which the R 7 substituent is attached. Thus, for example, compounds of Formulae I, II and III in which n is 0 and Z is -C(R 6

)(R

7 will have two chiral centers and can exist as four individual stereoisomers or any mixture thereof.

Individual stereoisomer may be characterized by the absolute configuration of their chiral centers.

Absolute configuration refers to the arrangement in space of the substituents attached to the chiral center. The substituents attached to the chiral center under consideration are ranked in accordance with the Sequence Rule of Cahn, Ingold and Prelog and then the absolute descriptor R is assigned if the three highest ranked substituents are arranged in space (with the fourth lowest ranked substituent directed away from the observer) from high to low priority in a clockwise sequence and the absolute descriptor S is assigned for a counterclockwise arrangement. When an individual stereoisomer containing one chiral center is described the absolute descriptor R or S is cited in parenthesis followed by a hyphen and the chemical name of the compound. For the purposes of this invention, when an individual stereoisomer or mixture of stereoisomers containing two or more chiral centers is described, the absolute descriptor R or S is cited immediately after the appropriate locant. Acyl radicals derived from naturally occurring amino acids are referred to as their amino acid radicals preceded by the descriptor L L-phenylalanine). The nonnatural enantiomers of amino acid acyl radicals are preceded by the descriptor D. Preferably, the amino acid side chains are the or L-form, due to the stereospecificity of enzymes, although the D-forms may be used in some cases. When no absolute descriptor is cited for a chiral center, the description is meant to include both configurations and WO 96/30353 PCT/US96/03844 12 mixtures thereof, racemic or otherwise. Thus, for example, a compound of the following formula: R7 H R' R' H 0 Re is named: N2-(4-morpholinylcarbonyl)-N'-[3-phenyl-1 S-(2-phenylsulfonylethyl)propyl]-L-phenylalaninamide, when R' is 4-morpholinylcarbonyl, R 8 is 2-phenylethyl and lies on the same side of the reference plane as the R 7 substituent, R 7 is benzyl and R 1 9 is phenylsulfonyl; MP-4-morpholinylcarbonyl-N'-[3-phenyl-1 -(2-phenylsulfonylethyl)propyl]-L-phenylalaninamide, when R' is 4-morpholinylcarbonyl, R' is 2-phenylethyl and lies on either or both sides of the reference plane, R 7 is benzyl and R 19 is phenylsulfonyl; IV A A-morprlinylcawronl-nh ny!1S (2i-Xp hnyrl lfonylethyu)rop!-13-(nahth )-alninmid when R' is 4-morpholinylcarbonyl, R 8 is 2-phenylethyl lies on the same side of the reference plane as the R 7 substituent, R 7 is 2-naphthylmethyl and R 19 is phenylsulfonyl and ethyl 4S-(N-4-morpholinylcarbonyl-L-phenylalanylamino)-6-phenylhexanoate, when R' is 4-morpholinylcarbonyl, R 8 is 2-phenylethyl and lies on the same side of the reference plane as the R 7 substituent, R 7 is benzyl and R 19 is ethoxycarbonyl.

In a preferred embodiment, the compositions of the invention are pure diasteromers. Alternatively, the compositions contain mixtures of diasteromers. Preferred embodiments have greater than about of a single disasteromer, with at least about 90% being particularly preferred.

"Protective group" has the meaning conventially associated with it in synthetic organic chemistry, i.e., a group which blocks a reactive site in a compound. See for example Greene et al., Protective Groups in Organic Synthesis, 2nd Ed., John Wiley Sons, 1991, hereby incorporated by reference.

Examples of hydroxy protective groups include heterocycloalkyl-carbonyl such as 4-morpholinylcarbonyl and the like, aroyl such as benzoyl and arylalkyl such as benzyl and the like.

Examples of amino protective groups include aryloxycarbonyl such as benzyloxycarbonyl and the like, aroyl such as benzoyl and the like and oxycarbonyl such as ethoxycarbonyl and 9-fluorenylmethoxycarbonyl and the like. Examples of guanidino protective groups include sulfonyl such as 2,3,5-trimethyl-4-methoxyphenyl-sulfonyl and the like. Examples of suitable carboxy protective groups that form ester moieties are alkoxylcarbonyl of overall 4 to 8 carbon atoms, particularly tert-butoxycarbonyl (BOC) or benzyloxycarbonyl (CBZ, especially cycloalkylaminocarbonyl or oxacycloalkylaminocarbonyl of overal 4 to 8 atoms in the ring, particularly 4-morpholinecarbonyl (Mu) and the like.

WO 96/30353 PCTIUS96/03844 13 "Protected" in reference to a compound of a group means a derivative of a compound or group in which a reactive site or sites are blocked with protective groups.

"Optional" or "optionally" means that the subsequently described event or circumstance may or may not occur, and that the description includes instances wherein the event or circumstance occurs and instances in which it does not. For example, "optionally further substituted with one or more functional groups" means that the substituents may or may not be present in order for the compound described to fall within the invention, and the invention includes those compounds wherein one or more functional groups are present and those compounds in which no functional groups are present.

By "cysteine protease-associated disorders" herein is meant pathological conditions associated with cysteine proteases. In some disorders, the condition is associated wtih increased levels of cysteine proteases; for example, arthritis, muscular distrophy, inflammation, tumor invasion, and glomerulonephritis are all associated with increased levels of cysteine proteases. In other disorders or diseases, the condition is associated with the appearance of an extracellular cysteine protease activity that is not present in normal tissue. In other embodiments, a cysteine protease is associated with the ability of a pathogen, such as a virus, to infect or replicate in the host organism.

Specific examples of cysteine protease associated disorders include, but are not limited to, arthritis, muscular distrophy, inflammation, tumor invasion, glomerulonephritits, malaria, Alzheimer's disease, cancer metastasis, trauma, inflammation, gingivitis, leishmaniasis, filariasis, and other bacterial and parasite-borne infections. In particular, disorders associated with interleukin 1p converting enzyme (ICE) are included.

"Pharmaceutically acceptable" means that which is useful in preparing a pharmaceutical composition that is generally safe, non-toxic and neither biologically nor otherwise undesirable and includes that which is acceptable for veterinary use as well as human pharmaceutical use.

"Pharmaceutically acceptable salts" means salts which are pharmaceutically acceptable, as defined above, and which possess the desired pharmacological activity. Such salts include acid addition salts formed with inorganic acids such as hydrochloric acid, hydrobromic acid, sulfuric acid, nitric acid, phosphoric acid, and the like; or with organic acids such as acetic acid, propionic acid, hexanoic acid, heptanoic acid, cyclopentanepropionic acid, glycolic acid, pyruvic acid, lactic acid, malonic acid, succinic acid, malic acid, maleic acid, fumaric acid, tartatic acid, citric acid, benzoic acid, o-(4-hydroxybenzoyl)benzoic acid, cinnamic acid, madelic acid, methanesulfonic acid, ethanesulfonic acid, 1,2-ethanedisulfonic acid, 2-hydroxyethanesulfonic acid, benzenesulfonic acid, p-chlorobenzenesulfonic acid, 2-naphthalenesulfonic acid, p-toluenesulfonic acid, camphorsulfonic

I

WO 96/30353 PCT/US96/03844 14 acid, 4-methylbicyclo[2.2.2]oct-2-ene-1-carboxylic acid, glucoheptonic aicd, 4,4'-methylenebis(3-hydroxy-2-ene-1-carboxylic acid), 3-phenylpropionic acid, trimethylacetic acid, tertiary butylacetic acid, lauryl sulfuric acid, gluconic acid, glutamic acid, hydroxynaphthoic acid, salicylic acid, stearic acid, muconic acid and the like.

Pharmaceutically acceptable salts also include base addition salts which may be formed when acidic protons present are capable of reacting with inorganic or organic bases. Acceptabale inorganic bases include sodium hydroxide, sodium carbonate, potassium hydroxide, aluminum hydroxide and calcium hydoxide. Acceptable organic bases include ethanolamine, diethanolamine, triethanolamine, tromethamine, N-methylglucamine and the like.

"Therapeutically effective amount" means that amount which, when administered to an animal for treating a disease includes: preventing the disease from occurring in an animal which may be predisposed to the disease but does not yet experience or display symptoms of the disease, inhibiting the disease, arresting its development, or ameliorate the disease, causing regression of the disease.

DETAILED DESCRIPTION OF THE INVENTION The present invention relates to novel cysteine protease inhibitors. Without being bound by theory, it is believed that the inhibitors bind to cysteine proteases based on the following scheme.

Enz Gln-H----0

R

2

R

7 Enz OB----H-His enzyme inhibitor A S- complex

R

Enz It is believed that the enzyme is thus reversibly inhibited by means of interactions between the R, Y and Z moieties of the inhibitor and the surface of the binding sites of the enzyme, and by means of hydrogen bonding interactions between the sulfone and active site amino acid side chains.

This mechanism of reversible inhibition permits specificity of the enzyme inhibitors for cysteine proteases. Generally, the inhibitors of the present invention inhibit cysteine proteases and do not inhibit serine, aspartyl, and zinc proteases. However, in some embodiments, the protease inhibitors of the present invention may have activity against other types of proteases, such as serine, aspartyl or

I

WO 96/30353 PCT/US96/03844 other metalloproteases, but to a lesser extent.

In addition, the electron withdrawing properties of the sulfone group of Formula I polarize the electrons between the sulfone group and the carbon to which it is attached, thus permitting hydrogen bonding between itself and active site residues of a cysteine protease, to allow tight binding between the inhibitor and the cysteine protease, as is generally described below. It is to be understood that there is presumably additional electron withdrawing or electron polarization occurring between the sulfur atom and the oxygen atoms, which allows the oxygen atoms to participate in hydrogen bonding with active site residues of the protease and thus contributing even further to the inhibition of the enzyme.

The present invention generally provides new peptide-based and peptidomimetic cysteine protease inhibitors for use as reversible cysteine protease inhibitors. By "cysteine protease inhibitor" herein is meant an inhibitor which inhibits cysteine proteases. In a preferred embodiment, the cysteine protease inhibitors are specific to cysteine proteases; that is, they do not inhibit other types of protease such as serine, aspartyl, or other metalloproteases. However, in alternative embodiments, the cysteine protease inhibitors of the invention may inhibit other types of proteases as well.

By "reversible" herein is meant that the inhibitor binds non-covalently to the enzyme, and is to be distinguished from irreversible inhibition. See Walsh, Enzymatic Reaction Mechanisms, Freeman Co., 1979. "Reversible" in this context is a term understood by those skilled in the art. In addition, the reversible cysteine protease inhibitors are competitive inhibitors, that is, they compete with substrate in binding reversibly to the enzyme, with the binding of inhibitor and substrate being mutually exclusive. In addition, the stoichiometry of inhibition is 1:1; that is, a single inhibitor molecule is sufficient to inhibit a single enzyme molecule.

The cysteine protease inhibitors herein are designed to bind reversibly to cysteine proteases. This binding is accomplished by using peptide-based or peptidomimetic structures as targeting groups that mimic naturally occurring substrates and/or inhibitors. "Peptidomimetic", for the purposes of this invention, means amino acid or peptide-like in structure but wherein one or more of the peptide linkages is substituted by an isosteric form, i.e. -CH 2 NR-, -C(O)CH 2 or -NRC(O)and/or wherein non-naturally occurring amino acid substituents are present.

"Targeting group", for the purposes of this application, means a peptide or peptidomimetic residue of the cysteine protease inhibitor that allows the binding of the inhibitor to a cysteine protease. In a preferred embodiment, the targeting group of a cysteine protease inhibitor comprises at least two amino acid side chains or side chain analogs, linked via a peptide bond or isostere. The targeting group may comprise up to about 15 amino acids or analogs, although inhibitors are generally from WO 96/30353 PCTfUS96/03844 16 about 1 to 7 amino acids or analogs, since smaller inhibitors are usually desired in therapeutic applications. Thus, in Formulae I, II and III, n is preferably from 0 to 13, with from 0 to 5 being preferred, and from 0 to 3 being particularly preferred.

As depicted in Formulae I, II and III, the targeting group can be represented by a naturally or non-naturally occurring peptide residue of the following formula:

R

7 R1R wherein the R 8 and R 7 components represent naturally or non-naturally occurring amino acid analogs or substituents as is more fully described below. The targeting group of the inhibitor may also contain additional functional groups, as depicted by R' and described herein.

While not being limited to any particular theory, it is believed that the amino acid substituents of the targeting group interact with the surface binding sites of the protease to promote binding. It is also believed that the amino acid substituent proximal to the electron withdrawing group R 8 of the above formula) will occupy the S, position of the substrate binding site and therefore is designated the P, residue of the inhibitor. Similarly, the next adjacent amino acid substituent R 7 of the above formula) will occupy the S2 position of the substrate binding site and is designated the P 2 residue of the inhibitor. If present, additional amino acid substituents will occupy the S3, S 4 etc. positions of the substrate binding site and be designated as the P 3

P

4 etc. residues of the inhibitor. An additional targeting group may be attached to the electron withdrawing group and, if present, its amino acid substituents will occupy the S2', etc. positions of the substrate binding sites and are designated the

P

3 P4', etc. residues of the inhibitor, respectively.

In general, targeting groups for specific enzymes are determined by rules governing substrate specificity in cysteine proteases see "Proteinase Inhibitors", in Research Monographs in Cell and tissue Physiology (1986), ed. Barret et al., Vol 12, Chapter 4: Inhibitors of Cysteine Proteinases, Daniel Rich, Elsevier, New York; and Thornberry et al., supra., hereby expressly incorporated by reference). For example, interleukin-1 converting enzyme (ICE) accepts an aspartic acid substituent 2-carboxyethyl) at the P, position and an alanine (methyl), valine (isopropyl) or histidine (4-imidazolylmethyl) substituent at the P 2 position. Papain accepts a arginine, lysine, Nbenzyloxycarbonyllysine 4-benzyloxycarbonylaminobutyl), homophenylalanine 2-phenylethyl), Guanidino-phenylalnine 4-guanidinobenzyl) or norluecine butyl) substitutents at the P, position and phenylalnine, tyrosine, p-)2-naphthyl)alanine 2-naphthyl), leucine, norleucine, WO 96/30353 PCTJUS96/03844 17 isoleucine or alanine substituents at the P 2 position. Cathepsin B accepts a arginine, lysine, Nbenzyloxycarbonyllysine, guanidino-phenylalanine, homophenylalanine or norleucine substituents at the P, position and phenylalanine, tyrosine, 3,5-diiodotyrosine 3,5-diiodo-4-hydroxybenzyl), naphthyl)alanine, arginine, guanidino-phenylalanine or citrulline 3-ureidopropyl) sybstituents at the P, position. Cathepsin L and cruzain accept arginine, lysine, homophenylalanine, guanindinophenylalanine, citrulline or norleucine substituents at the P, position and phenylalanine, tyrosine or P-(2-naphthyl)alanine substituents at the P 2 position. Cathepsin S accepts a arginine, lysine, homophenylalanine, guanidino-phenylalanine, citrulline or norleucine substituents at the P, position and phenylalanine, tyrosine, P-(2-naphthyl)anine, valine, leucine, norleucine, isoleucine or alanine substituents at the P, position. DPP-1 accepts phenylalanine or tyrosine substituents at the P, position and no subsuttuent or alanine at the P 2 position. Calpain accepts phenylalanine, tyrosine, methionine, 0-methylsulfonylmethylalanine 2-methylsulfonylethyl) or valine substituent at the P, position and vaiina leucine nnrleticine or isoleucine substituents at the P, position.

Thus, R 7 and RI are independently hydrogen, alkyl (optionally substituted with a radical selected from hydroxy, amino, alkylamino, dialkylamino, uriedo, mercapto, alkylthio, carboxy, carbamoyl, alkylcarbamoyl, dialkylcarbamoyl, alkylsulfonyl and guanidino, or a protected derivative thereof), cycloalkyl, cycloalkylalkyl, heteroaryl, heteroarylalkyl, a group selected from aryl and arylalkyl (which group is optionally substituted at its aryl ring with one to three radicals selected from hydroxy, amino, guanidino, halo, optionally halo-substituted alkyl, alkyloxy and aryl, or a protected derivative thereof) or together with an adjacent R 3 or R 5 forms a divalent radical selected from (C,,)methylene and 1,2-phenylenedimethylene (which radical is optionally substituted with hydroxy, or a protected derivative thereof, or oxo).

Accordingly, preferred R 7 and R' groups are the naturally occuring amino acid side chains and homologous derivatives. These include, but are not limited to, alanine (methyl), arginine (3guanidinopropyl), asparagine (carbamoylmethyl), cituriline (3-ureidopropyl), aspartic acid (carboxymethyl), cysteine (mercaptomethyl), glutamic acid (2-carboxyethyl), glutamine (2carbamoylethyl), glycine (hydrogen), histidine (4-imidazolylmethyl), homophenylalanine (2phenylethyl), homoserine (2-hydroxylethyl), isoleucine ((1-methylpropyl), leucine (isobutyl), lysine (4aminobutyl), methionine (2-methylthioethyl), P-(1-naphthyl)alanine (1-napthylmethyl), P-(2naphthyl)alanine (2-napthylmethyl), norleucine (butyl), norvaline (propyl), ornithine (3-aminopropyl), phenylalanine (benzyl), proline (as described herein), sarcosine (methylaminomethyl), serine (hydroxymethyl), threonine (1-hydroxyethyl), tryptophan (3-indolymethyl), tyrosine (4-hydroxybenzyl), and valine (isopropyl).

While the broadest definition of this invention is set forth in the Summary of the Invention, certain P:\OPER\DCD\53674-96.273 30/9/99 -18compounds of the invention are preferred. For example, generally preferred compounds of Formulae 1. 11 and IIl are those in which n is 0 to 5; A-B represents a linkage selected from -C(O)NR 3 wherein 3 is hydrogen or as defined below; Y is wherein R 5 is hydrogen or as defined below; Z is

-(CH

2 2 or Z' is RI is hydrogen, alkyloxycarboflylalkanoyl of overall3 to carbon atoms, (C 1 .,)alkoxycarbonyl,

(C

2 1 )alkanoyl (optionally substituted with a radical selected from carboxy, (C,.)alkyloxycarbonyl and hetero(C 4 .)cycloalkyl(C 2 .1o)alkaloylamnio). (C4)cycloalkylcarbonyl, hetero(C 4 .a)cycloalkylcarbonyl (optionally substituted with a radical selected from hydroxy, .00 (C 14 $)alkyl, (C 1 .,)alkanoyl. 5 )alkyloxycarbonyl. (C.)ayI(C.,)alkyloxycarbonyl and s*: 10 hetero(C 4 .)cycloalkylcarbonyl), (Cr, 10 )aryI(C 1 5 )alkyloxycarboflyl, carbarnoyl, 5 )alkylcarbamoyl, 00 di(C,.

5 )alkylcarbamnoyl. (C 6 1 )arylcarbamoyl, (C 6 1 )aryl(C.)alkylcarbanmoyl, (Cc 1 )aryl(C 15 )alkanoyl.

(C7, 1 )aroyl, (C,.,)alkylsuffonyl, di(C 15 )alkylaminosufonyl, 10 )arylsuffoflyl or hetero(Cs)arylsufofyl; 0and R 7 and Re are independently (C 1 5 )alkyl (optionally substituted with a radical selected from hydroxy, amino, alkylamino, dialkylamino. uriedo. mercapto, alkylthio. carboxy, carbamoyl.

:alkylcarbamoyl. dialkylcarbamoyl, alkylsulfonyl and guanidino, or a protected derivative thereof),

(C

3 .,)cycloalkyl. (C 37 )cycloalkyl(C 15 ,)akyl, pyridyl, thienyl. furyl, imidazolyl, indolyl. pyridyl(C 14 6)alkyl, thienyl(C, 14 )alkyl. furyl(C 14 ,)alkyl, imidazolyl(C 14 ,)alkyl. indolyl(C 4 )alkyl, a group selected from

(C

1 5 )alkyl, (C 2 -6)alkyloxy and (C 1 5 )alkanoyloxy (which group is optionally substituted with a radical selected from mercapto, carboxy, amino, methylthio, methylsulfonyl, carbanioyl, dimethylcarbamoyl, guanidino and hydroxy, or a protected derivative thereof), a group selected from phenyl, naphthyl, 20 phenyl(C 1 46alkyl, naphthyl(C 1 -6)alkyl, (which group is optionally substituted at its aryl ring with one to three radicals selected from hydroxy, amino, chloro, bromo, iodo, fluoro, methyl, trifluoromethyl, OS methoxy and phenyl, or a protected derivative thereof) or together with an adjacent RW or R 5 forms a 000 0 divalent radical selected fr-om (C 3 4 )methylene and 1 ,2-phenylenedimethylene (which radical is optionally substituted with hydroxy, or a protected derivative thereof, or oxo).

More preferred compounds of Formulae 1, 11 and Ill are those in which n is 0 to 2; A-B represents a lin'kage selected from -C(Q)NR 3 wherein R 3 is hydrogen or as defined below; Y is -N(R 5 wherein R is hydrogen or as defined below; Z is -(CH 2 2 or -C(R 6 (with the proviso that when n is 0, Z is not

-(CH

2 2 Z' is R' is hydrogen. (C 4 .a)alkoxycarbonyl, (C 2 .6)alkanoyl (optionally substituted with a radical selected from carboxy. (C 1 .)alkyloxycarbonyl and hetero(C41)cyCloalkyl(C4.) alkanoylamino). -C(O)NR 21 R22 wherein R 2 and R22 together form aza(C 2 6 S)methylene, Oxa(C 24 )methylene or (C3.7)methylene. (C,.a)cycloalkylcarbonyl, benzyloxycarbonyl, acetyl. benzoyl or .\dimfethylaminosulfonyl; and RO and R 7 are independently (Cs.)cycloalkyl. 3-pyridyl, 2-thienyl, 2-furyl, 4-imidazolyi, 3-indotyl, 3-pyridylmethyl, 2-thienylmethyl, P:\OPER\DCD\53674-96-273 30/9/99 18A 2-furylrflethyl4idazolyimietyl, 3-indolylmethyl, (C.s)alkyl (optionally substituted with a radical selected from mercapto, carboxy, amino, mnethylthio, methylsulfonyl, carbamoyl, dimethylcarbamoyl.

guanidino and hydroxy, or a protected derivative thereof), a group selected from phenyl, I-naphthyl, 2-naphthyl, benzyl, 1-naphthylmethyl, 2-naphthylmethyl and 2-phenylethyl (which group is optionally substituted at its aryl ring with one radical selected from hydroxy, amin6. chloro, bromo and fluoro. or a 00 9 *000 000: 00 0 0 0:0 @0 0000, WO 96/30353 PCTIUS96/03844 19 protected form thereof) or together with an adjacent R 3 or RI forms a divalent radical selected from

(C

3 z)methylene and 1,2-phenylenedimethylene (which radical is optionally substituted with hydroxy, or a protected derivative thereof, or oxo).

Particularly preferred compounds of Formulae 1, 11 and III are those in which n is 0 to 1; A-B represents a linkage selected from -C(O)NR 3 Y is -N(R 5 wherein R' is hydrogen or as defined below; Z is

-C(R

6 Z' is -CH(R 8 R' is hydrogen, tert-butoxycarbonyl, benzyloxycarbonyl, acetyl, 3-carboxypropionyl, 3-methoxycarbonylpropionyl, biotinylaminohexanoyl, phenylacetyl, benzoyl, dimethylaminosulfonyl, benzylsulfonyl, 1-piperazinylcarbonyl, 4-methylpiperazin- 1-ylcarbonyl or 4-morpholinylcarbonyl; R 7 is 3-pyridylmethyl, 2-thienylmethyl, 2-furylmethyl, 4-imidazolylmethyl, 3-indolylmethyl, (C, 5 )alkyl (optionally substituted with a radical selected from mercapto, carboxy, amino, methylthio, methylsulfonyl, carbamoyl, dimethylcarbamoyl, guanidino and hydroxy, or a protected derivative thereof), a group selected from benzyl, 1-naphthylmethyl, 2-naphthylmethyl and 2-phenylethyl (which group is optionally substituted at its aryl ring with one radical selected from hydroxy, amino, chloro, bromo and fluoro, or a protected form thereof) or together with an adjacent R 3 or R 5 forms a divalent radical selected from (C 34 )methylene and 1,2-phenylenedimethylene (which radical is optionally substituted with hydroxy, or a protected derivative thereof, or oxo); and R8 is butyl, 2-phenylethyl, 2-methylsulfonylethyl, 2-tert-butoxycarbonylethyl, 2-tert-butoxycarbonylmethyl, 4-tert-butoxycarbonylaminobutyl, 4-benzoylaminobutyl or benzyloxymethyl.

More particularly preferred compounds of Formulae 1, 11 and III are those in which n is 0; A-B represents a linkage selected from Y is Z is -CH(R 7 Z is -CH(R 5

R

1 is hydrogen, tert-butxoycarbonyl, benzyloxycarbonyl, biotinylaminohexanoyl, benzoyl, piperizin-1-ylcarbonyl, 4-methylpiperazin-1-ylcarbonyl or 4-morpholinylcarbonyl; R 7 is (C 1 -)alkyl, optionally substituted benzyl, 1-naphthylmethyl, 2-naphthylmethyl, 3-pyridinylmethyl or 2-methylsulfonylethyl; and RI is butyl, 2-phenylethyl or 2-methylsulfonylethyl.

Most preferred compounds of Formula 1, 11 and III are those in which n is 0; A-B represents a linkage selected from Y is Z is -CH(R 7

Z

1 is -CH(R 8 R' is 1-piperizinylcarbonyl, 4-methyl- 1-piperazinylcarbonyl or 4-morpholinylcarbonyl; R 7 is optionally substituted benzyl, 1-naphthylmethyl or 2-naphthylmethyl; and R 8 is 2-phenylethyl.

Generally preferred compounds of Formula I are those in which R 2 is independently 5 )alkyl (optionally substituted with one or two radicals selected from amino, chloro, bromo, fluoro, hydroxy and methoxy, or a protected derivative thereof), perhalo(C.

5 )alkyl, (C3-7)cycloalkyl,

(C

37 )cycloalkyl(Cl.

5 )alkyl or a group selected from phenyl, pentafluorophenyl, naphthyl and phenyl(C 1 -)alkyl (which group is optionally substituted at its aryl ring with one to two radicals selected WO 96/30353 PCT/US96/03844 from amino, chloro, bromo, fluoro, hydroxy, methoxy and optionally halo-substituted methyl, or a protected derivative thereof) and R 4 is hydrogen, (C, 5 )alkyl or (C 6 1 )aryl(C,.

5 )alkyl. More preferred compounds of Formula I are those in which in which R 2 is (Cis)alkyl (optionally substituted with one or two radicals selected from amino, chloro, bromo, fluoro and hydroxy, or a protected derivative thereof), perfluoro(C.s 5 )alkyl, (Cs.6)cycloalkyl, (C.6)cycloalkylmethyl or a group selected from phenyl, naphthyl and benzyl (which group is optionally substituted with one radical selected from amino hydroxy, chloro, bromo or fluoro, or a protected derivative thereof) and R 4 is hydrogen or methyl. Particularly preferred compounds of Formula I are those in which R 2 is methyl, trifluoromethyl, optionally substituted phenyl, 2-naphthyl or 2-phenylethyl. Most preferred compounds of Formula I in which R 2 is phenyl, 2-naphthyl or 2-phenylethyl, particularly phenyl or 2-naphthyl, and R 4 is hydrogen.

Generally preferred compounds of Formula II in which R 9 is -C(O)OR 1 0

-P(O)(OR

1 0 2 -S(O)(NRo)R 1 0

-C(O)NHC(O)R'

O or -S(O),NHC(O)Ro are those in which each R 1 0 is independently )lalkyl (optionally substituted with one or two radicals selected from amino, chloro, bromo, fluoro, hydroxy and methoxy or a protected derivative thereof), (C 3 7 )cycloalkyl, (C 3 7 )cycloalkyl(C,.,)alkyl, or a group selected from phenyl or phenyl(C, 1 .)alkyl (which group is optionally substituted at its phenyl ring with one to two radicals selected from amino, chloro, bromo, fluoro, hydroxy, methoxy and optionally halo-substituted methyl, or a protected derivative thereof). More preferred compounds of Formula II in which R 9 is -C(O)OR 10

-P(O)(OR

10 2

-S(O)(NR

0

)R

10

-C(O)NHC(O)R

10 or -S(0) 2

NHC(O)R

1 0 are those in which in which R 1 0 is ethyl, (C 5 s 6 )cycloalkyl, (C.

6 )cycloalkylmethyl or a group selected from phenyl and benzyl (which group is optionally substituted at its phenyl ring with one radical selected from amino hydroxy, chloro, bromo or fluoro, or a protected derivative thereof).

Generally preferred compounds of Formula II in which R 9 is C(O)R" or are those in which R" is 5 )alkyl, (C 3 7 )cycloalkyl, (C 37 )cycloalkyl(C,.

5 )alkyl or a group selected from phenyl and phenyl(C,.)alkyl (which group is optionally substituted at its aryl ring with one to two radicals selected from amino, chloro, bromo, fluoro, hydroxy, methyl, trifluoromethyl and methoxy). More preferred compounds of Formula II in which R" is C(O)R" or -S(O)R 11 are those in which in which R 1 is ethyl, cyclo(C 5 )alkyl, cyclo(Cs.

6 )alkylmethyl or a group selected from phenyl and benzyl (which group is optionally substituted at its phenyl ring with one radical selected from amino hydroxy, chloro, bromo or fluoro, or a protected derivative thereof).

Generally preferred compounds of Formula II in which R 9 is -C(O)NR 1 2

R

1 3 or -S(0) 2 NR1 2

R

13 are those in which R 1 2 and R 13 are independently (C 1 s)alkyl, (C 3 7 )cycloalkyl, (C 3 7 )cycloalkyl (C 1 s )alkyl or a group selected from phenyl and phenyl(C, 1 )alkyl (which group is optionally substituted at its phenyl ring with one to two radicals selected from amino, chloro, bromo, fluoro, hydroxy, methoxy and optionally halo-substituted methyl). More preferred compounds of Formula II in which R 9 is -C(O)NR 1 2

R

1 3 or WO 96/30353 PCTIUS96/03844 21

-S(O)NR

12 R3 are those in which R 12 and are independently ethyl, (C 5 ,)cycloalkyl, (C,-)cycloalkylmethyl or a group selected from phenyl and benzyl (which group is optionally substituted at its phenyl ring with one radical selected from amino hydroxy, chloro, bromo or fluoro, or a protected derivative thereof).

Preferred compounds of Formula II in which R 9 is -C(O)NHR 14 or -S(O),NHR 1 4 wherein R' 4 is a group selected from Formulae and are those in which each n, A, B, Y, Z, R' and R 10 are as defined above with respect to preferred compounds of Formulae I, II and Ill.

Generally preferred compounds of Formula Ill are those in which is a group selected from 2-furyl, 2-thienyl, 2-pyrrolyl, 2-phospholyl, 2-arsoyl, 3-pyridyl or 3-phosphorinyl (which group is optionally substituted with at least one radical selected from 5 )alkylcarbamoyl, di(C,.)alkylcarbamoyl, (Cr.-)alkyloycarbnyl, .)alkylsulfinamoyl, di(C,.

5 )alkylsulfinamoyl, (C,.,)alkylsulfonyl, carboxy, nitro, sulfinamoyl, sulfo, carbamoyl, phosphono, (C 15 )alkyloxyphosphinyl, di(C,.

5 )alkyloxyphosphinyl, (C,-,)alkanoyl, cyano, (C,-,)alkylsulfinyl, sulfamoyl, (C, 5 )alkylsulfamoyl, di(Cl- 5 )alkylsulfamoyl,

(C

1 5 )alkyloxysulfonyl, phenyl, naphthyl, pyridyl, thienyl, furyl, imidazolyl, indolyl, hydroxy,

(C,

1 )alkyloxy, optionally halo-substituted (C,-)alkyl, benzyl, halo, -'N(R 7 wherein each R" 7 is independently (C,.,)alkyl, phenyl or benzyl, or -N(R 8 2 wherein each R 18 is independently hydrogen,

(C,

5 )alkyl, phenyl or benzyl). More preferred compounds of Formula III are those in which R 1 6 is a group selected from 2-furyl, 2-thienyl, 2-pyrrolyl, 2-phosholyl, 2-arsolyl, 3-pyridyl or 3-phosphorinyl (which group is optionally substituted with at least one radical selected from methylcarbamoyl, dimethylcarbamoyl, methyloxycarbonyl, methylsulfinamoyl, dimethylsulfinamoyl, methylsulfonyl, carboxy, nitro, sulfinamoyl, sulfo, carbamoyl, phosphono, methyloxyphosphinyl, dimethyloxyphosphinyl, formyl, cyano, methylsulfinyl, sulfamoyl, methylsulfamoyl, dimethylsulfamoyl, methoxysulfonyl, methylsulfonimidoyl, phenyl, naphthyl, pyridyl, thienyl, furyl, imidazolyl, indolyl, hydroxy, methoxy, methyl, trifluromethyl, benzyl, halo, 7 3 wherein each R 17 is independently methyl, phenyl or benzyl, or -N(R"3) 2 wherein each R18 is independently hydrogen, methyl, phenyl or benzyl). Generally preferred compounds of Formula III in which R' 6 is a group selected from Formulae and are those in which each n, A, B, Y, Z, R' and R' 0 are as defined above with respect to preferred compounds of Formulae 1, II and Ill.

In general, preferred cysteine protease inhibitors of the invention are those in which the absolute configuration of each chiral center present is the (S)-configuration. However, preferred compounds of Formula I in which n is 0 are those in which the absolute configuration of chiral center to which the R 7 substituent is attached is in the (R)-configuration. For example, preferred compounds of Formula I include: \P-(4-morpholinylcarbonyl)-N'-(3-phenyl-1 R-phenylsulfonylpropyl)-L-phenylalaninamide (compound AP-(4-morpholinylcarbonyl)-N 1 -(3-phenyl-l S-phenylsulfonylpropyl)-L-phenyalaninamide WO 96/30353 PCTIUS96/03844 22 (compound AM-(4-morpholiflylcarboflyl)-t-(3-pheflYl -phenylsulfonylpropyl)-L-pheflylalaniflamide (compound M\P(4-morpholinylcarboflyl)-M\-(3-phenyl-I -benzylsulfonylpropyl)-L-leuciflamide (compound M\P(4-morpholinylIca rboflyl)-MVl-(3-phenyl-l -trifluoromethylsulfonylpropyl)- L-phenylalaniflamide (compound M\P(4-morpholinylcarbofl)-N 1 '-(3-pheflyl-l -benzylsulfonylpropyl)- L-phenylalaninamide (compound M\P(4-morpholinylcarboflyl).Nl'(3-phellphenyisulfonylpropyl)- L-leucinamide (compound AM-(4-morpholiflylcarboflyl)-AN1(3-pheflyl-lfluoromethylsulfonylpropyl)- L-phenylalaninamide (compound /\P(4-morpholiflylcarbonyl)-MV-(3-phenyl- 1 S-phenylsulfonylmethylpropyl)-Lphenylalaniamide (compound M\-(4-morpholinylcarbonyl)- M\-{3-phenyl-1 S-[2-(2-phenylethylsulfonyl)ethylI propyl}-L-phenylalaninamide (compound M\P(4-morpholinylcarbonyl)-NV'-{3-phenyl-I S-[2-(2-naphthylsulfonyl)ethyl~propyl}-I3-(2-naphthyl)- L-alaninamide (compound 11); AP-phenylacetyl-AI'-[3-phenyl-l S-(2-phenylsulfonylethyl)propyII- L-phenylalaninamide (compound 12), MV2(N-benzyloxycarbonyi-p-alanyl)-Nr-[ 3 -phenyl- 1 S~2~phnyisifoniethi~pr pyiLhenyiainninamidep (CoCmDound 13). 34{2-phenyl-1 S-[3-phenyl- 1 S-(2-phenylsulfonylethyI)propylcarbamoyl]ethylcarbamoyl}propionic acid (compound 14); 3-{2-naphthyl-1 S-[3-phenyl-1 S-(2-phenylsulfonylethyl)propylcarbamoylI ethylcarbamoyl}propionic acid (compound 15); M\P(4-morpholinylcarbonyl)-AM-{3-phenylI S-[2-(2-naphthylsulfonyl)ethylIpropyl}- L-tyrosinamide (compound 16); methyl 3-{2-phenyl-1 S-[3-phenyI- 1 S-(2-phenylsulfonylethyl)propylcarbamoyl]ethylcarbamoyl)propionate (compound 17); /\P(4-morpholinylcarbonyl)-N 1 -[3-phenyl-I S-(2-phenylsulfonyethyl)propyl]-Lphenylalaninamide (compound 18); M\-(D3.alanyI)-NV 1 -[3-phenyl-1 S-(2-phenylsulfonylethyl) propyl]-L-phenylalaninamide (compound 19); and 5-phenylsulIfonyl-3 S-N[-NaeyILt oyl-Lvli--lnlmn~aei acid (compound 20). Preferred compounds of Formula 11 include: ethyl 4S-(N-benzylsulfonyl- D-2npty)Laayaio--hnleaot (compound 21); ethyl 4S-(N-benzylcarbamoyl- 0-2npty)Laayaio--hnleaot (compound 22); ethyl 4S[-4mrhlnlabnl---nphhlLaayaio--hnieaot (compound 23); ethyl 4S(-ezlabmy--hnlaayaio--hnleaot (compound 24); ethyl 4S[-4mrhlnlabnl--heyaayaio--hnleaot (compound M\P(4-morpholinylcarbonyI)-M-[3-phenyl-1 S-(2-phenylcarbamoylethyl)propyl]-L-phenylalaninamide (compound 26); and M-(4-morpholinylcarbonyl)-/A43phenyl-l S-(2-benzylcarbamoyiethyl)propy]- L-phenylalaninamide (compound 27). Preferred compounds of Formula IlI include: M-(4-morpholinylcarbonyl)-NI(3-phenyl-l S-2(-ehxpey~ty~rpl--hnlinnmd (compound 28); and M\P(4-morpholinylcarbonyl)-/N 1 {3-phenyl-l S-[2-(4-aminophenyl)ethyl]propyl)- L-phenylalaninamide (compound 29).

As will be appreciated by those in the art, Formula I includes structures represented by preferred WO 96/30353 PCT/US96/03844 23 Species IV as depicted below.

R

7 R

B

M A I'R 2

RI

IV

wherein M is zero, one or two carbon atoms, A-B are as defined above, R 1

R

2

R

7 and R 8 are as defined above, and Q is NH or CH 2 Preferred embodiments utilize A-B linkages which contain nitrogen at the B position. In this embodiment, the number of carbon atoms between the carbon to which the R" group is attached and the sulfur atom of the sulfone group determines whether the compound is an a-aminosulfone, a p-aminosulfone, or a y-aminosulfone. As is discussed below in the Examples, compounds may be named as aminosulfones using the names of the amino acids or using the chemical names.

Thus, for example, Species V is an a-aminosulfone:

R

7 0 R B S 2 ,A B I R

R

8

V

Species VI is a p-aminosulfone:

R

7 R B IKR

R

8 0

VI

Species VII is a y-aminosulfone: R O0 1

A

Y' 0

R

8

VII

Formula II includes structures of Species VIII, referred to as y-amino groups, particularly when R 9 is an electron withdrawing group:

VIII

WO 96/30353 PCTIUS96/03844 24 In a preferred embodiment, the dissociation constant for inhibition of a protease with an inhibitor of the invention, generally referred to by those in the art as K, is at most 100 pM. By the term "binding constant" or "dissociation constant" or grammatical equivalents herein is meant the equilibrium dissociation constant for the reversible association of inhibitor with enzyme. The dissociation constants are defined and determined as below.

The determination of dissociation constants is known in the art. For example, for reversible inhibition reactions such as those of the present invention, the reaction scheme is as follows: Equation 3 E+I E The enzyme and the inhibitor combine to give an enzyme-inhibitor complex, E.l. This step is assumed to be rapid and reversible, with no chemical changes taking place; the enzyme and the inhibitor are held together by non-covalent forces. In this reaction, k, is the second order rate constant for the formation of the E'1 reversible complex, k 2 is the first order rate constant for the disassociation of the reversible E-I complex. In this reaction, K, k 2 The measurement of the equilibrium constant K, proceeds according to techniques well known in the art, as described in the examples. For example, assays generally use synthetic chromogenic or fluorogenic substrates.

The respective K, values may be estimated using the Dixon plot as described by Irwin Segel in Enzyme Kinetics: Behavior and analysis of rapid equilibrium and steady-state enzyme systems, 1975, Wiley-lnterscience Publication, John Wiley Sons, New York, or for competitive binding inhibitors from the following calculation: Equation 4 1-(vJv) wherein v, is the rate of substrate hydrolysis in the absence of inhibitor, and vi is the rate in the presence of competitive inhibitor.

It is to be understood that dissociation constants are a particularly useful way of quantifying the WO 96/30353 PCTIUS96/03844 efficiency of an enzyme with a particular substrate or inhibitor, and are frequently used in the art as such. If an inhibitor exhibits a very low it is an efficient inhibitor. Accordingly, the cysteine protease inhibitors of the present invention have dissociation constants, of at most about 100 pM. Preferred embodiments have inhibitors that exhibit dissociation constants of at most about 10 pM, with the most preferred embodiments having dissociation constants of at most about 1 pM.

CHEMISTRY

The synthesis of the inhibitors of the invention proceeds as follows. Compounds of Formula I in which X represents a bond can be prepared by the process depicted in Scheme 1 of Figure 1.

Treatment of tert-butylcarbamate or benzyl carbamate with an appropriate aldehyde, such as isobutyraldehyde or hydrocinnamaldehyde, along with the sodium salt of a suitable sulfinic acid, such as benzenesulfinic acid (Aldrich Chemical in the presence of aqueous formic acid affords the corresponding N-protected aminomethyl sulfone. Benzyloxycarbonyl protected aminomethyl sulfones are deprotected with hydrogen bromide in acetic acid. Coupling with a suitable N-protected amino acid or peptide or a peptidomimetic derivative thereof affords a compound of Formula I in which X represents a bond. Alternatively, an appropriate N-terminal protected amino acid or peptide of peptidomimetic derivative thereof, such as N-(4-morpholinylcarbonyl)phenylalaninamide, is reacted with an appropriate aldehyde along with the sodium salt of a suitable sulfinic acid, in the presence of aqueous formic acid to afford a compound of Formula I in which X represents a bond.

Compounds of Formula 1 in which X represents a methylene bond can be prepared by the processes depicted in Schemes 2 and 3, Figures 2 and 3, respectively.

Treatment of a suitable N-protected amino acid or peptidomimetic derivative thereof with sodium borohydride affords the corresponding p-aminoethanol. Treatment of the alcohol with methanesulfonyl chloride in the presence of triethylamine affords the corresponding mesylate. Nucleophilic displacement with the anion of a thiol, such as thiophenol, according to the method of Spaltenstein, A., Carpion, Miyake, and Hopkings, J. Org. Chem (1987) 52, 3759, affords the corresponding P-aminosulfide. The sulfide is oxidized by means of 4-chloroperbenzoic acid to give the corresponding N-protected P-aminoethyl sulfone. In a special instance, the mesylate is treated with thiolate ion such as that derived from 2-(trimethylsilyl)ethanethiol, the synthesis of which is described by Anderson, Ranasinghe, Palmer, Fuchs, J. Org. Chem. (1988) 53, 3125, to give the corresponding p-aminoethyl 2-trimethylsilylethyl sulfide. The 2-trimethylsilylethyl sulfide is reduced to the corresponding p-aminoethyl 2-trimethylsilylethyl sulfone, which is then subjected to fluoride-mediated cleavage, extruding trimethylsilyl fluoride and ethene as gaseous by-products, and WO 96/30353 PCT/US96/03844 26 an intermediate sulfinate, which sulfinate is alkylated in situ with an appropriate halogen-containing species such as bromochloromethane to give the corresponding N-protected 1-aminoethyl halomethyl sulfone. The N-protected P-aminoethyl sulfones are deprotected and then coupled with a suitable N-protected amino acid or peptide or a peptidomimetic derivative thereof to afford a compound of Formula I in which X is methylene.

Compounds of Formula II and Formula I in which X represents ethylene can be prepared by the processes depicted in Equations 5, 6 and 7.

Equation 0

H

Bo-HOH

K

0

H

BoA-N

O

8 a)

R

0

H

b)

K-

h/ i 8 wherein a) is a) CI-H 2 N+(Me)OMe, dicyclohexylcarbodiimide, triethylamine; and b) lithium aluminum hydride.

Equation 6 0

H

Boc-N R8 0 R'O1 R'O

EWG

RO

H

R"

R E P+ EWG

X_

Boc-N EWG

H

Boc--N EWG Equation 7 H,/Pd

H

BocR--N EW

R

8 An appropriate N-tert-butoxycarbonyl amino acid or peptidomimetic derivative thereof is converted to the corresponding aminomethyl aldehyde see method of Fehrentz, J-A. and Castro, B.

(Synthesis, (1983), 676; Equation The aldehyde is converted to the corresponding vinylogous compound via aWittig reaction or a Wadsworth-Emmons-Horner modification of the Wittig reaction see Wadsworth et al., J. Amer. Chem. Soc. 83: 1733 (1991); Equation The vinylogous compound is reduced by catalytic hydrogenation see Equation 7) and then deprotection and coupling with a suitable N-protected amino acid or peptide or a peptidomimetic derivative thereof gives WO 96/30353 PCT/US96/03844 27 the corresponding compound of Formula I or II. Alternatively, the vinylogous compound is deprotected and coupled with the N-protected amino acid or peptide or a peptidomimetic derivative thereof to give the corresponding vinyloguous condensation product, which is then reduced to give the corresponding compound of Formula I or II.

Compounds of Formula II can be prepared by the processes depicted in Scheme 4, Figure 4.

Preferably, the conversion of N-tert-butoxycarbonyl amino acid or peptidomimetic derivative thereof to the corresponding aminomethyl aldehyde is carried out with N,O-dimethylhydroxylamine hydrochloride in the presence of triethylamine and dicyclohexylcarbodiimide in dicloromethane. Alternatively, the conversion is carried out by treating the amino acid or peptidomimetic derivative with triethylamine and the coupling agent benzotriazol-1-yloxytris(dimethylamino)phosphonium hexafluorophosphate (BOP) and then reducing with lithium aluminum hydride to aive the corresponding aldehyde see methos of Fehrentz, J-A. and Castro, Synthesis, (1983), 676-678). The conversion of the aldehyde to the corresponding vinylogous ester can be carried out with the sodium anion of triethyl phosphonoacetate.

Deprotection of the vinylogous ester can be carried out with hydrogen chloride in dioxane. The hydrogenation is typically carried out in the presence of palladium.

Compounds of Formula I in which X is ethylene are conveniently prepared by the process depicted in Scheme 5, Figure Treatment of a suitable N-tert-butoxycarbonyl-a-aminoaldehyde, prepared as described in Equation with the sodium anion of an appropriate sulfonylmethanephosphonate (SMP) diethyl phenylsulfonylmethanephosphonate, diethyl 2-naphthylsulfonylmethane-phosphonate, diethyl methylsulfonylmethanephosphonate, etc.) gives the corresponding vinylogous sulfone. The sulfone is deprotected with anhydrous p-toulenesulfonic acid in ether and then coupled with N-protected amino acid or peptide or a peptidomimetic derivative thereof to give the corresponding vinyloguous condensation product, which is then reduced to give the corresponding compound of Formula I.

Suitable arylsulfonylmethanephsophonates can be prepared by treating arylthiols with paraformaldehyde in the presence of hydrogen chloride and reacting with triethyl phosphite to give the corresponding diethyl phsophonomethyl aryl sulfide and then oxidizing the sulfide. Alternatively, suitable sulfides can be obtained commercially diethylphosphonomethyl methyl sufide obtained from Aldrich Chemical Co., diethylphosphonomethyl phenyl sulfide, etc.) and oxidized to their corresponding sulfones.

Compounds of Formula II in which R 9 is -COOH can be prepared by the process depicted in Scheme 6, Figure 6.

I

WO 96/30353 PCT/US96/03844 28 Generally, saponification of a compound of Formula II in which R 9 is -COOR 1 0 results in the cooresponding carboxylate, which upon treatment with acid gives the corresponding carboxylic acid.

Compounds of Formula II in which R 9 is -P(O)(R 1 0 2 can be prepared as depicted in Scheme 7 (Figure 7) by proceeding as in Scheme 6, but substituting for the SMP the sodium anion of an appropriate methylenediphosphonate tetraethyl methylenediphosphonate, etc.).

Compounds of Formula II in which R 9 is -C(O)NHR 14 can be prepared as depicted in Scheme 8 (Figure 8) by proceeding as in Scheme 5, but substituting for the SMP an appropriate diethyl amidomethylenephsophonate diethyl benzylamidomethylenephosphonate, etc.).

Suitable amidomethylenephosphonates can be prepared by reacting the saponification product of triethyl phosphonoacetate with an appropriate amine. Altenatively, compounds of Formula II in which

R

9 is -C(O)NHR 14 can be prepared by reacting a compound of Formula I in which R 9 is -COOH with an appropriate amine. For example, the reaction can be carried out in the presence of dicyclohexylcarbodiimide in dichloromethane or by any other peptide coupling reaction sequences known to those of skill in the art.

In general, compounds of Formula II can be prepared by the process depicted in Scheme 9 (Figure 9) and substituting the starting materials represented by Structures I-VII.

Structure I C 0 0 Synthesis of ketones is performed by means of the Wadsworth-Emmons reaction between Boc-aamino aldehydes and the appropriate phosphonate, followed by catalytic reduction with hydrogen in the presence of palladium. Generally, the aldehyde portion is synthesized as outlined above. The phosphonate, if not commercially available, is synthesized by treatment of the enolate anion of methyl or substituted methyl ketones, such as acetone or acetophenone, with diethyl chlorophosphonate.

The enolate anion is generated, for example, by treatment of a tetrahydrofuran solution of diisopropylamine with butyllithium, followed by addition of the ketone to the lithium diisopropylamide (LDA) solution House, Modern Synthetic Reactions, 2nd Ed. Benjamin, Inc., Menlo Park, CA, Chapter Following formation of the enolate, diethyl chlorophosphonate is added. The Wadsworth-Emmons reagent forms as a consequence of coupling of the enolate with diethyl chlorophosphate.

I

WO 96/30353 PCTUS96/03844 29 For the synthesis of cysteine protease inhibitors with nitriles as the EWG, structure II is used: Structure II 0 P C-N Synthesis of nitriles is performed by means of the Wadsworth-Emmons reaction between Boc-aamino aldehydes and the appropriate phosphonate, followed by hydrogenation in the presence of a suitable catalyst. Generally, the aldehyde portion is synthesized as outlined above. The phosphonate is commercially available.

For the synthesis of cysteine protease inhibitors with sulfoxides as the EWG, structure III is used: Structure III 0 0 C, I 1 Ci0"/P S R' Synthesis of sulfoxides is performed by means of the Wadsworth-Emmons reaction between Boc-aamino aldehydes and the appropriate phosphonate, followed by hydrogenation in the presence of a suitable catalyst. Generally, the aldehyde portion is synthesized as outlined above. The phosphonate is synthesized by treatment of the anion of methyl sulfoxides with diethyl chlorophosphate. The anion is generated by addition of BuLi to diisopropylamine, followed by addition of the methyl sulfoxide.

For the synthesis of cysteine protease inhibitors with sulfonamides as the EWG, structure IV is used: Structure IV O O

C,H

5 II CH0O 1P ]NHR" 4

O

Synthesis of sulfonamides is performed by means of the Wadsworth-Emmons reaction between Boca-amino aldehydes and the appropriate phosphonate, followed by hydrogenation in the presence of a suitable catalyst. Generally, the aldehyde portion is synthesized as outlined above. The phosphonate is synthesized, for instances, by a method such as the following: a) diethylphosphoryl methanesulfonates, as prepared by the method of Carretero and Ghosez (Tetrahedron Lett., 28:1104- 1108 (1987)), are converted to sulfonyl chlorides by treatment with phosphorus pentachloride (M.

Quaedvlieg, in "Methoden der Organische Chemic (Houben-Weyl)", ed. E. Muller, Thieme Verlag, Stuttgart, 4th Ed., 1955, Vol. IX, Chapter 14); or b) treatment of the sulfonyl chloride with an amine, WO 96/30353 PCT/US96/03844 such as ammonia, a primary amine (including an amino acid derivative), or a secondary amine, that results in the formation of the sulfonamide (Quaedvlieg, supra, Chapter 19). The sulfonamidephosphonate is then reacted with Boc-a-aminoaldehydes to form the target compounds as per the Wadsworth-Emmons reaction.

For the synthesis of cysteine protease inhibitors with sulfinamides as the EWG, structure V is used: Structure V 0 0 O O P o\ CH0o P S NHi2 Synthesis of sulfinamides is performed by means of the Wadsworth-Emmons reaction between Boc-aamino aldehydes and the appropriate phosphnnnte followed by hydrnoenation in the presenr.e of a suitable catalyst. Generally, the aldehyde portion is synthesized as outlined above. The phosphonate may be synthesized using one of the following methods. Treatment of methyl dialkyl phosphonates such as the commercially available methyl diethyl phosphonate (Aldrich), with thionyl chloride in the presence of aluminum chloride gives the dialkylphosphoryl methanesulfinyl chloride (Vennstra et al., Synthesis (1975) 519. See also Anderson, "Comprehensive Organic Chemistry (Pergamon Press)", Vol. 3, Chapter 11.18, (1979). Alternatively, treatment of the dialkyl phosphoryl sulfinyl chloride with amines (Stirling, Internat. J. Sulfur Chem. 6:277 (1971)), yields the dialkyl phosphoryl sulfinamide.

For the synthesis of cysteine protease inhibitors with sulfoximines as the EWG, structure VI is used: Structure VI O O P S-R

R

1 0 Synthesis of sulfoximines is performed by means of the Wadsworth-Emmons reaction between Boc-aamino aldehydes and the appropriate phosphonate, followed by hydrogenation in the presence of a suitable catalyst. Generally, the aldehyde portion is synthesized as outlined above. The phosphonate may be synthesized in several ways. For example, N-alkyl or N-aryl phenyl methyl sulfoximines are made by the methods described by Johnson, in "Comprehensive Organic Chemistry (Pergamon Press), supra, Chapter 11.11. Alternatively, the lithium anion of compounds such as N-alkyl phenyl methyl sulfoximine is prepared by the treatment of the neutral compound with buthyl lithium in THF (Cram et J. Amer. Chem. Soc. 92:7369 (1970)). Reaction of this lithium anion with dialkyl chlorophosphates such as the commercially available diethyl chlorophosphate (Aldrich) results in the

I

Wadsworth-Emmons reagent necessary for synthesis of the sulfoximine compounds.

For the synthesis of cysteine protease inhibitors with sulfonates as the EWG, structure VII is used: Structure VII 0 P SO,-M+ Synthesis of sulfonates is performed by means of the Wadsworth-Emmons reaction between Boc-aamino aldehydes and the appropriate phosphonate, for instance diethylphosphoryl methanesulfonate, followed by hydrogenation in the presence of a suitable catalyst, such as Raney nickel. The phosphonate may be synthesized as follows. The anion of methyl dialkyl phosphonates such as the commercially available methyl diethyl phosphonate (Aldrich) is generated by treatment of said phosphonate with a strong base such as LDA. The resulting anion is sulfonated with sulfur trioxide/trimethylamine complex (Carreto et al., Tetrahedron Lett., 28:1104-1108 (1987)) to form diethylphosphoryl methanesulfonate, which is capable of reacting in the Wadsworth-Emmons procedure with aldehydes to form a,1-unsaturated sulfonates.

Compounds of Formula II can be prepared by the process depicted in Scheme 10 (Figure The chloride compounds containing Re and R 9 groups are generally made using commercially o available reagents and products using techniques well known in the art. The reaction generally produces a mixture of cis and trans configurations, favoring the trans isomer. Upon reduction to the cysteine protease inhibitors of this embodiment, the cis-trans isomerism disappears by definition as a single compound is formed.

In one embodiment, the cysteine protease inhibitors of the invention are further purified if necessary after synthesis, for example to remove unreacted materials. For example, the cysteine protease *inhibitors of the present invention may be crystallized, or passed through silica chromatography columns using solvent mixtures to elute the pure inhibitors.

In summary, the processes for preparing compounds of the invention are as follows: for the preparation of Formula IV: O R& n

IH

WO 96/30353 PCTIUS96/03844 32 in which n is 0 to 12; R 2 0 is cyano, -S(O) 2

R

2

-CH

2

S(O),R

2

-CH

2 CH(R )S(O) 2

R

2

-(CH

2 2

C(O)OR'

0

-(CH

2 2

P(O)(OR'

0

-(CH

2 2

S(O)(NR'O)R

1 0

-CH

2 2

C(O)R

1 1

-(CH

2 2

S(O)R

1

-(CH

2 2

C(O)NR

1 2

R

1 3

-(CH

2 2 S(0) 2

NR

2

R

1 3

-(CH

2 2

C(O)NHR

1 4

-(CH

2 2 S(0) 2

NHR

14 or -CH 2

CHR

1 5

R

6 and each A, B, X, Y, Z,

R

1

R

8

R

1

R

8

R

2 Ro, R 1 1

R

1 2

R

13 R R 1 and R' 6 are as defined in the Summary of the Invention with respect to compounds of Formulae I, II and III, and the pharmaceutically acceptable salts, individual isomers and mixtures of isomers thereof, reacting an amine of Formula V: H,N -j

R

2 0 with a compound of the Formula VI: o R- Z A L u A Z n

H

VI

in which each n, A, B, X, Y, Z, R" and R 20 are as defined above; for the preparation of a compound of Formula IV in which R 2 0 is -S(0) 2

R

2 and the pharmaceutically acceptable salts, individual isomers and mixtures of isomers thereof, reacting a compound of Formula VII: 0 RI Z A B A Z NH

VII

with an aldehyde of the formula R 8 CHO and a sodium sulfinate of the formula R 2 S(O)ONa, in which each n, A, B, X, Y, Z, R 1 and R 8 are as defined above; for the preparation of a compound of Formula IV in which R 20 is -S(0) 2

R

2 and the pharmaceutically acceptable salts, individual isomers and mixtures of isomers thereof, reacting a compound of the formula NH 2 P, wherein P is a protective group, with an aldehyde of the formula R 8 CHO and a sodium sulfinate of the formula R 2 S(O)ONa and then deprotecting to give a compound of Formula VIII:

R

8 H2N S(O) R 2 WO 96/30353 PCT/US96/03844 33 in which each R 2 and R 8 are as defined in the Summary of the Invention with respect to Formula I; and reacting the compound of Formula VIII with a compound of Formula VI in which each n, A, B, X, Y, Z and R 1 are as defined above; for the preparation of a compound of Formula IV in which R 2 0 is -CH 2

S(O)

2

R

2 and the pharmaceutically acceptable salts, individual isomers and mixtures of isomers thereof, reacting a compound of Formula

IX:

R

PHN

with a thiolate anion of the formula R 2 S, in which L is a leaving group R 2 and R 8 are as defined above, to give a compound of Formula X:

R

1 SR2

PHN

oxidizing the compound of Formula X to give a compound of Formula XI: Ra PHN S(O) 2

R

2 PHN and reacting the compound of Formula XI with a compound of Formula VI in which each n, A, B, X, Y, Z and R' are as defined above; for the preparation of a compound of Formula IV in which R 20 is cyano, -(CH 2 2

S(O)

2

R

2

-(CH

2 2

C(O)OR

1 o, -(CH 2 2

P(O)(OR

10 2

-(CH

2 2

S(O)(NR

0

)R

1 0

-(CH

2 2

-(CH

2 2

S(O)R

1

-(CH

2 2

C(O)NR

12

R

1 3

-(CH

2 2 S(0) 2

NR

1 2

R

13

-(CH

2 2

C(O)NHR

14 or -(CH 2 2 S(0) 2

NHR

1 4 and the pharmaceutically acceptable salts, individual isomers and mixtures of isomers thereof, reacting an aldehyde of Formula XII:

R"

PHN

CHO

with a compound selected from Formulae XIII and XIV: 0

R

2 R 210 0 R 20

R

2 1 0 R

R

2 1 XIII

XIV

in which each R 8 and R 2 0 are as defined above, and then deprotecting to give a

I

WO 96/30353 PCTIUS96103844 34 compound of Formula XV:

XV

reacting the compound of Formula XV with a compound of Formula VI in which each n, A, B, X, Y, Z and R 1 are as defined above, and reducing; for the preparation of a compound of Formula IV in which R 2 0 is -CH 2

CHR'R

1 6 and the pharmaceutically acceptable salts, individual isomers and mixtures of isomers thereof, reacting an aldehyde of Formula XII with compound of Formula XVI:

R.

P(Ph) 3

R

16

XVI

in which each R 8

R

15 and R'6 are as defined above, and then deprotecting to give a compound of Formula XVII:

R

8 NR

R'

6

XVII

reacting the compound of Formula XVII with a compound of Formula VI in which each n, A, B, X, Y, Z and R 1 are as defined above, and reducing; optionally further converting a non-salt form of a compound of Formula IV into a pharmaceutically acceptable salt; optionally further converting a salt form of a compund of Formula IV into non-salt form; and optionally further separating a compound of Formula IV into individual stereoisomers.

In one embodiment, the cysteine protease inhibitors of the present invention are labelled. By a "labelled cysteine protease inhibitor" herein is meant a cysteine protease inhibitor that has at least one element, isotope or chemical compound attached to enable the detection of the cysteine protease inhibitor or the cysteine protease inhibitor bound to a cysteine protease. In general, labels fall into three classes: a) isotopic labels, which may be radioactive or heavy isotopes; b) immune labels, which WO 96/30353 PCTIUS96/03844 may be antibodies or antigens; and c) colored or fluorescent dyes. The labels may be incorporated into the cysteine protease inhibitor at any position. For example, a label may be attached as the "R 1 group in Formula 1, or a radioisotope incorporated into any position. Examples of useful labels include 14 C, 3 H, biotin, and fluorescent labels as are well known in the art.

PHARMACOLOGY AND UTILITY Once produced, the cysteine protease inhibitors of the present invention may be easily screened for their inhibitory effect. The inhibitor is first tested against the cysteine protease for which the targeting group of the inhibitor was chosen, as outlined above. Alternatively, many cysteine proteases and their corresponding chromogenic substrates are commercially available. Thus, a variety of cysteine proteases are routinely assayed with synthetic chromogenic substrates in the presence and absence of the cysteine protease inhibitor, to confirm the inhibitory action of the compound, using techniques well known in the art. The effective inhibitors are then subjected to kinetic analysis to calculate the K, values, and the dissociation constants determined.

If a compound inhibits at least one cysteine protease, it is a cysteine protease inhibitor for the purposes of the invention. Preferred embodiments have inhibitors that exhibit the correct kinetic parameters against at least the targeted cysteine protease.

In some cases, the cysteine protease is not commercially available in a purified form. The cysteine protease inhibitors of the present invention may also be assayed for efficacy using biological assays.

For example, the inhibitors may be added to cells or tissues that contain cysteine proteases, and the biological effects measured.

In one embodiment, the cysteine protease inhibitors of the present invention are synthesized or modified such that the in vivo and in vitro proteolytic degradation of the inhibitors is reduced or prevented. Generally, this is done through the incorporation of synthetic amino acids, derivatives, or substituents into the cysteine protease inhibitor. Preferably, only one non-naturally occurring amino acid or amino acid side chain is incorporated into the cysteine protease inhibitor, such that the targeting of the inhibitor to the enzyme is not significantly affected. However, some embodiments that use longer cysteine protease inhibitors containing a number of targeting residues may tolerate more than one synthetic derivative. In addition, non-naturally occurring amino acid substituents may be designed to mimic the binding of the naturally occurring side chain to the enzyme, such that more than one synthetic substituent is tolerated. Alternatively, peptide isosteres are used to reduce or prevent inhibitor degradation.

WO 96/30353 PCT/US96/03844 36 In this embodiment, the resistance of the modified cysteine protease inhibitors may be tested against a variety of known commercially available proteases in vitro to determine their proteolytic stability.

Promising candidates may then be routinely screened in animal models, for example using labelled inhibitors, to determine the in vivo stability and efficacy.

Specific cysteine proteases that may be inhibited by the inhibitors of the present invention are those of the family of cysteine proteases that bear a thiol group at the active site. These proteases are found in bacteria, viruses, eukaryotic microorganisms, plants, and animals. Cysteine proteases may be generally classified as belonging to one of four or more distinct superfamilies. Examples of cysteine proteases that may be inhibited by the novel cysteine protease inhibitors of the present invention include, but are not limited to, the plant cysteine proteases such as papain, ficin, aleurain, oryzain and actinidain; mammalian cysteine proteases such as cathepsins B, H, J, L, N, S, T, 0, and C, (cathepsin C is also known as dipeptidyl peptidase interleukin converting enzyme (ICE), calcium-activated neutral proteases, calpain I and II; bleomycin hydrolase, viral cysteine proteases such as picornian 2A and 3C, aphthovirus endopeptidase, cardiovirus endopeptidase, comovirus endopeptidase, potyvirus endopeptidases I and II, adenovirus endopeptidase, the two endopeptidases from chestnut blight virus, togavirus cysteine endopeptidase, as well as cysteine proteases of the polio and rhinoviruses; and cysteine proteases known to be essential for parasite lifecycles, such as the proteases from species of Plasmodia, Entamoeba, Onchocera, Trypansoma, Leishmania, Haemonchus, Dictyostelium, Therileria, and Schistosoma, such as those associated with malaria falciparium), trypanosomes cruzi, the enzyme is also known as cruzain or cruzipain), murine P. vinckei, and the C. elegans cysteine protease. For an extensive listing of cysteine proteases that may be inhibited by the cysteine protease inhibitors of the present invention, see Rawlings et al., Biochem. J. 290:205-218 (1993), hereby expressly incorporated by reference.

Accordingly, inhibitors of cysteine proteases are useful in a wide variety of applications. For example, the inhibitors of the present invention are used to quantify the amount of cysteine protease present in a sample, and thus are used in assays and diagnostic kits for the quantification of cysteine proteases in blood, lymph, saliva, or other tissue samples, in addition to bacterial, fungal, plant, yeast, viral or mammalian cell cultures. Thus in a preferred embodiment, the sample is assayed using a standard protease substrate. A known concentration of cysteine protease inhibitor is added, and allowed to bind to a particular cysteine protease present. The protease assay is then rerun, and the loss of activity is correlated to cysteine protease activity using techniques well known to those skilled in the art.

The cysteine protease inhibitors are also useful to remove or inhibit contaminating cysteine proteases in a sample. For example, the cysteine protease inhibitors of the present invention are added to samples where proteolytic degradation by contaminating cysteine proteases is undesirable.

I WO 96/30353 PCTIUS9603844 37 Alternatively, the cysteine protease inhibitors of the present invention may be bound to a chromatographic support, using techniques well known in the art, to form an affinity chromatography column. A sample containing an undesirable cysteine protease is run through the column to remove the protease.

In a preferred embodiment, the cysteine protease inhibitors are useful for inhibiting cysteine proteases implicated in a number of diseases. In particular, cathepsins B, L, and S, cruzain, calpains I and II, and interleukin 11 converting enzyme are inhibited. These enzymes are examples of lysosomal cysteine proteases implicated in a wide spectrum of diseases characterized by tissue degradation.

Such diseases include, but are not limited to, arthritis, muscular dystrophy, inflammation, tumor invasion, glomerulonephritis, parasite-borne infections, Alzheimer's disease, periodontal disease, and cancer metastasis. For example, mammalian lysosomal thiol proteases play an important role in intracellular degradation of proteins and in the processing of some peptide hormones. Enzymes similar to cathepsins B and L are released from tumors and may be involved in tumor metastasis.

Cathepsin L is present in diseased human synovial fluid and transformed tissues. Similarly, the release of cathepsin B and other lysosomal proteases from polymorphonuclear granulocytes and macrophages is observed in trauma and inflammation.

The cysteine protease inhibitors also find application in a multitude of other diseases, including, but not limited to, gingivitis, malaria, leishmaniasis, filariasis, and other bacterial and parasite-borne infections.

The compounds also offer application in viral diseases, based on the approach of inhibiting proteases necessary for viral replication. For example, many picornoviruses including poliovirus, foot and mouth disease virus, and rhinovirus encode for cysteine proteases that are essential for cleavage of viral polyproteins.

Additionally, these compounds offer application in disorders involving interleukin-1R converting enzyme (ICE), a cysteine protease responsible for processing interleukin 111; for example, in the treatment of inflammation and immune based disorders of the lung, airways, central nervous system and surrounding membranes, eyes, ears, joints, bones, connective tissues, cardiovascular system including the pericardium, gastrointestinal and urogenital systems, the skin and the mucosal membranes. These conditions include infectious diseases where active infection exists at any body site, such as meningitis and salpingitis; complications of infections including septic shock, disseminated intravascular coagulation, and/or adult respiratory distress syndrome; acute or chronic inflammation due to antigen, antibody and/or complement deposition; inflammatory conditions including arthritis, chalangitis, colitis, encephalitis, endocarditis, glomerulonephritis, hepatitis, myocarditis, pancreatitis, pericarditis, reperfusion injury and vasculitis. Immune-based diseases include but are not limited to conditions involving T-cells and/or macrophages such as acute and WO 96/30353 PCT/US96/03844 38 delayed hypersensitivity, graft rejection, and graft-versus-host disease; auto-immune diseases including Type I diabetes mellitus and multiple sclerosis. Bone and cartilage reabsorption as well as diseases resulting in excessive deposition of extracellular matrix such as interstitial pulmonary fibrosis, cirrhosis, systemic sclerosis, and keloid formation may also be treated with the inhibitors of the present invention. The inhibitors may also be useful in the treatment of certain tumors that produce IL 1 as an autocrine growth factor and in preventing the cachexia associated with certain tumors. Apoptosis and cell death are also associated with ICE and ICE-like activities and may be treated with the inhibitors of the present invention Furthermore, the cysteine protease inhibitors of the present invention find use in drug potentiation applications For example, therapeutic agents such as antibiotics or antitumor drugs can be inactivated through proteolysis by endogeneous cysteine proteases, thus rendering the administered drug less effective or inactive. For example, it has been shown that bleomycin, an antitumor drug, can be hydrolyzed by bleomycin hydrolase, a cysteine protease (see Sebti et al., Cancer Res. January 1991, pages 227-232). Accordingly, the cysteine protease inhibitors of the invention may be administered to a patient in conjunction with a therapeutic agent in order to potentiate or increase the activity of the drug. This co-administration may be by simultaneous administration, such as a mixture of the cysteine protease inhibitor and the drug, or by separate simultaneous or sequential administration.

In addition, cysteine protease inhibitors have been shown to inhibit the growth of bacteria, particularly human pathogenic bacteria (see Bjorck et al., Nature 337:385 (1989)). Accordingly, the cysteine protease inhibitors of the present invention may be used as antibacterial agents to retard or inhibit the growth of certain bacteria.

The cysteine protease inhibitors of the invention also find use as agents to reduce the damage of bacterial cysteine proteases to host organisms. For example, staphylococcus produces a very active extracellular cysteine protease which degrades insoluble elastin, possibly contributing to the connective tissue destruction seen in bacterial infections such as septicemia, septic arthritis and otitis.

See Potempa et al., J. Biol. Chem. 263(6):2664-2667 (1988). Accordingly, the cysteine protease inhibitors of the invention may be used to treat bacterial infections to prevent tissue damage.

ADMINISTRATION AND PHARMACEUTICAL COMPOSITION In general, cysteine protease inhibitors of this invention will be administered in therapeutically effective amounts via any of the usual and acceptable modes known in the art, either singly or in combination with another cysteine protease inhibitor of the invention or with another therapeutic agent. A WO 96/30353 PCT/US96/03844 39 therapeutically effective amount may vary widely depending on the severity of the disease, the age and relative health of the subject, the potency of the compound used and other factors.

Therapeutically effective amounts of the cysteine protease inhibitors of this invention may range from micrograms per kilogram body weight (pg/kg) per day to 10 milligram per kilogram body weight (mg/kg), typically 100 pg/kg/day to 1 mg/kg/day. Thus, a therapeutically effective amount for a 80 kg human may range from 1 mg/day to 1000 mg/day, typically 10 mg/day to 100 mg/day.

One of ordinary skill in the art of treating such diseases will be able, without undue experimentation and in reliance upon personal knowledge and the disclosure of this application, to ascertain a therapeutically effective amount of a cysteine protease inhibitor of this invention for a given disease.

In general, the cysteine protease inhibitors of this invention will be administered as pharmaceutical compositions by one of the following routes: oral, systemic transdermal, intranasal, intrapulmonary, or by suppositiory) or parenteral intramuscular, intravenous, intrapulmonary or subcutaneous). Compositions can take the form of tablets, pills, capsules, semisolids, powders, sustained release formulations, solutions, suspensions, elixiers, aerosols or any other appropriate composiiton and are comprised of, in general, a cysteine protease inhibitor of the invention in combination with at least one pharmaceutically acceptable excipient. Acceptable excipients are non-toxic, aid administration, and don not adversely affect the therapeutic benefit of the cysteine protease inhibitor of this invention. Such excipient may be any solid, liquid, semisolid or, in the case of an aerosol composition, gaseous excipient that is generally available to one of skill in the art.

Solid pharmaceutical excipients include starch, cellulose, talc, glucolse, lactose, sucrose, gelatin, malt, rice, flour, chalk, silica gel, magnesium stearate, sodium sterate, glycerol monostearate, sodium chloride, dried skim milk and the like. Liguid and semisolid excipients may be selected from water, ethanol, glycerol, propylene glycol and various oils, includingthose of petroleum, animal, vegetable or synthetic origin peanut oil, soybean oil, mineral oil, sesame oil, etc.). Preferred liquid carriers, particularly for injectable solutions, include water, saline, aqueous dextrose and glycols.

Compressed gases may be used to disperse the cysteine protease inhibitor of this invention in aerosol form. Inert gases suitable for this purpose are nitrogen, carbon dioxide, nitrous oxide, etc. Other suitable pharmaceutical carriers and their formulations are described in A.R. Alfonso Reminton's Pharmaceutical Sciences 1985, 17th ed. Easton, Pa.: Mack Publishing Company, hereby expressly incorporated by reference.

The amount of a cysteine protease inhibitor of this invention in the composition may vary widely depending upon the type of formulation, size of a unit dosage, kind of excipients and other factors WO 96/30353 PCT/US96/03844 known to those of skill in the art of pharmaceutical sciences. In general, the final composition will comprise from 0.1%w to 10%w of the cysteine protease inhibitor, preferably 1%w to 10%w, with the remainder being the excipient or excipients.

Preferably the pharmaceutical composition is administered in a single unit dosage form for continuous teatment or in a single unit dosage form ad libitum when relief of symptoms is specifically required.

Representative pharmaceutical formulations containing a cysteine protease inhibitor of the invention are described in Example 20, infra.

The following examples serve to more fully describe the manner of using the above-described invention, as well as to set forth the best modes contemplated for carrying out various aspects of the invention. It is understood that these examples in no way serve to limit the true scope of this invention, but rather are presented for illustrative purposes. All references cited herein are expressly incorporated by reference.

EXAMPLES

The following abbreviation conventions have been used to simplify the examples.

Mu morpholine urea Xaa, amino acid at P1 position relative to active site of the enzyme Xaa 2 amino acid at P2 position relative to active site of the enzyme y-CO 2 Et= y-amino ethyl ester y-SO 2 Ph= y-aminosulfone with phenyl terminus y-CO 2 H y-aminocarboxylate y-PEt y-aminophosphonate y-AM y-aminoamide y-Ar(sub)= y-aminoaromatic compound (substituted as appropriate)

P-SO

2 Ph= p-aminosulfone with phenyl substituent a-SO 2 Ph= a-aminosulfone with phenyl substituent Hph homophenylalanine PSMP diethyl phenylsulfonylmethylenephosphonate Np2 2-naphthylalanine

SO

2 2Np sulfone with 2-maphthyl terminus Phac phenylacetyl B-Ala B-alanine MeOSuc methoxysuccinyl WO 96/30353 PCTUS96/03844 41 For instance, Mu-Phe-Hph-p-SO 2 Ph where Xaa 2 Phe (phenylalanine) and Xaa, Hph (homophenylalanine,), transformed to the p-amino phenyl sulfone according to the procedure described in the Examples.

Example 1 Synthesis of Cysteine Protease Inhibitor Containing a y-aminoester as the EWG Unless otherwise indicated, all reactions were performed under an inert atmosphere of argon or nitrogen at room temperature. THF was distilled from sodium benzophenone ketyl. All other solvents and commercially available reagents were used without further purification.

Synthesis of Ethyl (.S)-4-(4-mrnholinecarbonyl-phenylalanyl)-amino-6-phenylhexanoate, abbreviated Mu-Phe-Hph-y-CO 2 Et, was as follows. Unless otherwise noted, all reagents were obtained from Aldrich, Inc. 0.393 g of a 60% mineral oil dispersion (9.82 mmol) of sodium hydride was added to a solution of triethyl phosphonoacetate (2.20 g, 9.82 mmol) in THF (50 mL) at-10 0 C. The mixture was stirred for 15 minutes, whereupon a solution of Boc-homophenylalaninal (Boc-HphH) (2.35 g, 9.82 mmol, prepared by conversion of Boc-homophenylalanine (Synthetech) to its N,O-dimethylhydroxamide, using the Fehrentz method. followed by lithium aluminum hydride reduction) in THF (20 mL) was added. The mixture was stirred for 45 minutes. 1M HCI (30 mL) was added. The product was extracted with ethyl acetate (50 mL), washed with saturated aqueous NaHCO 3 (30 mL) dried over MgSO 4 filtered, and evaporated to dryness. The dried material was dissolved in CH 2

CI

2 (10 mL), and a 4.0 M solution of HCI in dioxane (20 mL) was added. The mixture was stirred for 30 minutes. The solvents were removed under reduced pressure and the residue, ethyl (S)-4-amino-6-phenyl-2-hexenoate hydrochloride, was pumped dry.

4-Morpholinecarbonylphenylalanine (Mu-PheOH, 2.74 g, 9.82 mmol, prepared according to the method described in Esser, R. et.al., Arthritis Rheumatism (1994), 37, 236) was dissolved in THF mL) at -10°C. 4-methylmorpholine (1.08 mL, 9.82 mmol) was added, followed by isobutyl chloroformate (1.27 mL, 9.82 mmol). The mixed anhydride was stirred for 10 minutes, whereupon a solution of ethyl (S)-4-amino-6-phenyl-2-hexenoate hydrochloride from the previous step in DMF mL) was added, followed by 4-methylmorpholine (1.08 mL, 9.82 mmol). The mixture was stirred for 1 hour. 1M HCI (50 mL) was added. The product was extracted with ethyl acetate (100 mL), washed with saturated aqueous NaHCO 3 (50 mL), dried over MgSO 4 and decolorizing charcoal (DARCO), filtered, and evaporated to dryness, giving 3.80 g of intermediate (80% yield from Boc-homophenylalaninal).

I

WO 96/30353 PCT/US96/03844 42 To a solution of this intermediate (1.45 g, 3.09 mmol) in ethanol (25 mL) was added 5% palladium on active carbon (0.5 The mixture was reduced on a Parr hydrogenator for 36 hours. The solution was filtered and the solvent was removed under reduced pressure, giving 1.19 g of the product.

Thin-layer chromatography (TLC) was performed on each sample. Visualization was accomplished by means of UV light at 254 nm, followed by ninhydrin, bromocresol green, or p-anisaldehyde stain. The retention factor (Rf) of the Mu-Phe-Hph-y-CO 2 Et was 0.35 MeOH/CH 2

CI).

NMR spectra were recorded on a Varian Gemini 300 MHz instrument. All 1 H NMR data of this and subsequent examples are reported as delta values in parts per million relative to internal tetramethylsilane, peak assignments in boldface. The following abbreviations are used: s, singlet; d, doublet; t, triplet; q, quartet; br, broad. An asterisk implies that a signal is obscured or buried under another resonance.

Example 2 Synthesis of a Cysteine Protease Inhibitor containing a y-aminosulfone as the EWG.

Synthesis of (S)-3-tert-butoxycarbonylamino-5 -phenyl-phenylsulfonylpentane (Boc-Hph-y-SO 2 Ph).

To a solution of PSMP (8.87 g, 30.34 mmol) in THF (150 mL) at 0°C was added sodium hydride (1.21 g of a 60% mineral oil dispersion). The mixture was stirred for 20 minutes, whereupon a solution of Boc-homophenylalaninal, synthesized by the method of Fehrentz and Castro, above, (7.99 g, 30.34 mmol) in THF (20 mL) was added. The solution was stirred for 30 minutes at 0°C. 1M HCI (100 mL) was added. The product was extracted into ethyl acetate (100 mL), washed with saturated aqueous sodium bicarbonate (100 mL), brine (50 mL), dried over MgSO 4 filtered, and the solvent was removed under reduced pressure. The residue was dissolved in ethanol (100 mL) and transferred to a Parr bottle charged with 5% palladium on active charcoal (0.92 The mixture was reduced on a Parr apparatus for 24 hours. The solution was filtered through Celite and the solvent was removed under reduced pressure. TLC of the product indicated a single product in quantitative yield, Rf 0.29 ethyl acetate/hexane) that stained white with paraanisaldehyde spray.

Example 3 Synthesis of a Cysteine Protease Inhibitor containing a y-aminosulfone as the EWG.

Synthesis of (S)-3-amino-5-phenyl-1-phenylsulfonyl-pentane hydrochloride (HCI.Hph-y-SO 2 Ph). To a solution of Boc-Hph-y-SO 2 Ph (12.24 g, 30.34 mmol) in dichloromethane (20 mL) was added hydrogen chloride in dioxane (50 mL of a 4.0M solution). The mixture was stirred for 90 minutes. The solvent was removed under reduced pressure, and the residue was dissolved in CH 2

CI

2 (50 mL). The solution WO 96/30353 PCTIUS96/03844 43 was carefully added to ether (500 mL) with stirring. The solid was filtered, washed with ether (50 mL) and dried in vacuo.

Example 4 Synthesis of a Cysteine Protease Inhibitor containing a y-aminosulfone as the EWG.

Synthesis of (S)-3-(4-morpholinecarbonylphenylalanyl)-amino-5-phenyl-l-phenylsulfonylpentane (Mu- Phe-Hph-y-SO 2 Ph). To a solution of Mu-PheOH (2.94 g, 10.56 mmol) in THF (75 mL) at -10 0 C were added 4-methylmorpholine (1.16 mL, 10.56 mmol) and isobutyl chloroformate (1.37 mL, 10.56 mmol).

The mixture was stirred for 5 minutes. (S)-(E)-3-amino-5-phenyl-1-phenylsulfonyl-1-pentene ptoluenesulfonate, synthesized by Wadsworth-Emmons condensation between Bochomophenylalaninal and p-toluenesulfonic acid deprotection (5.00 g, 10.56 mmol) was added, followed by 4-methylmorpholine (1.16 mL, 10.56 mmol). The mixture was stirred for 45 minutes. The solution was diluted with ethyl acetate (100 mL), washed with 1M HCI (2x50 mL), saturated aqueous sodium bicarbonate (50 mL), brine (50 mL), dried over MgSO 4 filtered, and the solvent was removed under reduced pressure. The residue was crystallized from CH 2

CI

2 /ether to give 4.27 g of intermediate. 1.17 g of this material (2.08 mmol) was dissolved in ethanol (25 mL). The solution was transferred to a Parr bottle charged with 5% palladium on active charcoal (0.30 The mixture was hydrogenated at room temperature overnight on a Parr shaker. Ethyl acetate was added to the suspension of product, which had crystallized from the reaction mixture. The solution was filtered and concentrated in vacuo, and then was recrystallized from CH 2 Cl 2 /hexane. M.p. 176-178 0 C. TLC: ethyl acetate/CH 2

CI

2 Rf 0.24.

Example Synthesis of a Cysteine Protease Inhibitor containing a y-aminosulfone as the EWG.

Synthesis of (S)-3-(4-morpholinecarbonyltyrosyl)-amino-5-phenyl- -phenylsulfonylpentane (Mu-Tyr- Hph-y-SO 2 Ph). To a solution of 4-morpholinecarbonyltyrosine (Mu-TyrOH, synthesized according to the method described in Esser, R. et.al., Arthritis Rheumatism (1994), 37, 236, 0.50 g, 1.70 mmol) in THF (10 mL) at -10°C were added 4-methylmorpholine (0.187 mL, 1.70 mmol) and isobutyl chloroformate (0.220 mL, 1.70 mmol). After 5 minutes, HCI.Hph-y-SO 2 Ph (0.577 g, 1.70 mmol, described in Example 3) was added, followed by 4-methylmorpholine (0.187 mL, 1.70 mmol). The mixture was stirred for 45 minutes. Ethyl acetate (50 mL) was added. The solution was washed with 1M HCI, saturated aqueous sodium bicarbonate, and brine (30 mL each), dried over MgSO 4 filtered, and the solvent was removed under reduced pressure. The residue was precipitated from

CH

2 Cl 2 ether to give 0.58 g of Mu-Tyr-Hph-y-SO 2 Ph. M.p. 104-107 0 C. TLC: MeOH/CH 2

CI

2 R, 0.59.

I

WO 96/30353 PCT/US96/03844 44 Example 6 Synthesis of a Cysteine Protease Inhibitor containing a y-aminosulfone as the EWG.

Synthesis of (S)-3-(4-morphlinecarbonyl-2-naphthyl-alanyl)amino-5-phenyl-1-(2naphthylsulfonyl)pentane (Mu-Np2-Hph-y-SO 2 2Np). 2-naphthalenethiol (9.64 g, 60.16 mmol) was dissolved in toluene (75 mL). Paraformaldehyde (3.97 g, 132 mmol) and HCI/dioxane (33 mL of a solution) were added. The mixture was stirred for several days at room temperature. The solvent was removed under reduced pressure, and the residue was suspended in hexane (200 mL), dried over MgSO 4 filtered, and evaporated to dryness. This material, crude chloromethyl 2-naphthyl sulfide, was combined with triethyl phosphite (10.93 g, 65 mmol) and was heated at reflux for 4 hours.

The mixture was cooled to room temperature, diluted with ether (200 mL), washed with 1M HCI, saturated aqueous sodium bicarbonate, and brine (150 mL each), dried over MgSO 4 filtered, and concentrated in vacuo to give 17.35 g (93% crude yield) of diethyl 2-naphthylthiomethylene phosphonate. This material was dissolved in CH 2

CI

2 (300 mL) and cooled to 0°C. Peracetic acid (23.5 mL of a 32% dilute acetic acid solution (Aldrich Chemical Co.) was carefully added. The mixture was stirred overnight while warming to room temperature. The solution was washed with freshly prepared, saturated aqueous sodium bisulfite solution (100 mL), then with several portions of saturated aqueous sodium bicarbonate, until the aqueous phase became basic. The organic phase was dried over MgSO 4 filtered, and the solvent was removed under reduced pressure. Chromatography on 60-200 mesh silica gel (0-10% ethyl acetate!CH 2

CI

2 afforded 6.5 g of the pure Wadsworth-Emmons reagent, diethyl 2-naphthylsulfonyl-methylene phosphonate along with an approximately equal mass of impure material. TLC: (20% ethyl acetate/CH 2

CI

2 R, 0.37.

To a solution of diethyl 2-naphthylsulfonylmethylene phosphonate (3.91 g, 11.42 mmol) in THF mL) at 0°C was added sodium hydride (0.457 g of a 60% mineral oil dispersion. The mixture was stirred for 15 minutes, whereupon a solution of Boc-homophenylalaninal (3.00 g, 11.42 mmol) in THF mL) was added. The mixture was stirred for 30 minutes. 1M HCI (100 mL) was added. The product was extracted with ethyl acetate (100 mL), washed with saturated aqueous sodium bicarbonate (75 mL), brine (50 mL), dried over MgSO 4 filtered, and the solvent was removed under reduced pressure. The residue was dissolved in dichloromethane (10 mL), to which was added HCI/dioxane (25 mL of a 4.0M solution). The mixture was stirred at room temperature for 1 hour, poured into ether (300 mL), and filtered. The solids were washed with ether (2x50 mL) and dried in vacuo to give 3.30 g (74% from Boc-homophenylalaninal) of (S)-(E)-3-amino-5-phenyl-1-(2naphthylsulfonyl)-1-pentene.

To a solution of Boc-2-naphthylalanine (2.68 g, 8.51 mmol, (Synthetech, Oregon) in THF (50 mL) at 0 C were added 4-methylmorpholine (0.936 mL, 8.51 mmol) and isobutyl chloroformate (1.103 mL, WO 96/30353 PCT/US96/03844 8.51 mmol). The mixture was stirred for 5 minutes, whereupon (S)-(E)-3-amino-5-phenyl-1-(2naphthylsulfonyl)-1-pentene (3.30 g, 8.51 mmol) was added, followed by 4-methylmorpholine (0.936 mL, 8.51 mmol). The mixture was stirred for 45 minutes, diluted with ethyl acetate (100 mL), washed with 1M HCI (50 mL), saturated aqueous sodium bicarbonate (50 mL), and brine (50 mL), dried over MgSO,, filtered, and the solvent was removed under reduced pressure. The intermediate, (tert-butoxycarbonyl-2-naphthylalanyl)amino-5-phenyl-1-(2-naphthylsulfonyl)-1-pentene, was crystallized from a suitable mixture CH 2 Cl 2 /ether/hexane in 69% yield. The resulting material (3.83 g, 5.90 mmol) was dissolved in CH 2

CI

2 (5 mL) and was treated with HCI/dioxane (15 mL of a solution. The mixture was stirred at room temperature for 1 hour. The solution was poured, with stirring, into ether (500 mL) and filtered. The solids were washed with ether (2x50 mL) and dried in vacuo to give the intermediate, (S)-(E)-3-(2-naphthylalanyl)-amino-5-phenyl-l-(2-naphthylsulfonyl)-1pentene, 3.41g, 99% yield.

2.00 g of this material (3.42 mmol) was dissolved in THF (15 mL), and cooled to 0°C. 4methylmorpholine-carbonyl chloride (0.400 mL, 3.42 mmol) and triethylamine (0.953 mmol) were added. The mixture was stirred for 1 hour at 0°C, and then at room temperature for 2 hours. Ethyl acetate (50 mL) was added. The solution was washed with 1M HCI (30 mL), saturated aqueous sodium bicarbonate (30 mL), brine (30 mL), dried over MgSO 4 filtered, and evaporated to dryness, giving 1.58 g of intermediate, (S)-(E)-3-(4-morpholinecarbonyl-2-naphthylalanyl)amino-5phenyl-1-(2-naphthylsulfonyl)-1-pentene. TLC: (50% ethyl acetate/hexane) Rf 0.37.

0.73 g (1.10 mmol) of this material was dissolved in ethanol (20 mL) and transferred to a Parr bottle charged with 5% palladium on carbon (0.30 The mixture was reduced on a Parr hydrogenator for 36 hours. The solution was filtered and the solvent was removed under reduced pressure. The product was purified by column chromatography on 60-200 mesh silica gel (50% ethyl acetate/CH 2

CI

2 as eluent) to give 0.14 g of pure product, Mu-Np2-Hph-y-SO22Np, along with impure material.

TLC: (50% ethyl acetate/CH 2

CI

2 R, 0.34.

Example 7 Synthesis of a Cysteine Protease Inhibitor containing a y-aminosulfone as the EWG.

Synthesis of 3-acetyltyrosylvalylalanylamino-4-hydroxy-carbonyl-1-phenylsulfonylbutane (Ac-Tyr-Val- Ala-Asp-y-SO 2 Ph). Sodium hydride (0.489 g of a 60% mineral oil dispersion, 12.23 mmol) was added to a solution of diethyl phenylsulfonylmethylene phosphonate (3.58 g, 12.23 mmol) in 50 mL of THF at 0°C. The mixture was stirred for 15 minutes. A solution of Boc-AspH(B-Ot-Bu), (3.04 gm, 11.12 mmol, prepared by converting Boc-Asp(P-O-t-Bu) to its N,O-dimethyldroxamide and reducing with lithium aluminum hydride), in THF (10 mL) was added. The mixture was stirred for 1 hour, whereupon

I

WO 96/30353 PCTJUS96/03844 46 1M HCI (30 mL) was added. The product was extracted with ethyl acetate (100 mL), washed with saturated aqueous NaHCO 3 (30 mL), brine (30 mL), dried over MgSO,. filtered, and evaporated to dryness, giving the intermediate,. Chromatography on silica gel (20-30% ethyl acetate/hexane, gradient elution) afforded 2.07 g 45%) of the intermediate, (S)-(E)-3-tert-butoxycarbonylamino-4-tertbutoxycarbonyl-l-phenylsulfonyl-l-butene. This material was dissolved in ether (2 mL) and was treated with a solution of anhydrous p-toluenesulfonic acid (1.0 g, 5.87 mmol) in ether (2 mL). The mixture was stirred at room temperature overnight, then diluted with ether (25 ml). The white precipitate, was filtered, washed with ether, and dried in vacuo to give 0.80 g of the next intermediate, (S)-(E)-3-amino-4-tert-butoxycarbonyl-1-phenylsulfonyl-1-butene-p-toluenesulfonate.

This material was coupled, using mixed anhydride chemistry, to Ac-Tyr-Val-AlaOH, itself prepared by standard peptide chemistry, giving the next intermediate, (S)-(E)-3-acetyltyrosylvalylalanylamino-4tert-butoxycarbony!-1-pheny!sulfony!-1-butene.

This material was treated with trifluoroacetic acid to remove the t-butyl ester of the aspartic acid side chain, giving (E)-3-acetyltyrosylvalylalanylamino-4-hydroxycarbonyl-1-phenylsulfonyl-1-butene. 0.28 g (0.444 mmol) of this material was dissolved in ethanol (10 mL). The solution was transferred to a Parr bottle, charged with 5% palladium on carbon (0.1 The solution was reduced on a Parr hydrogenator overnight. The solution was filtered and the solvent was removed under reduced pressure. The residue, when dissolved in methanol (5 mL) and diluted with 40x 1:1 CH 2

CI

2 /ether, formed a gelatinous precipitate, which was collected on a Buchner funnel to give 0.18 g yield.

The isomer ratio of S to R with respect to the Asp residue was estimated as approximately 3:1 based on the integration of the doublets associated with the aromatic region of the NMR as pertains to the Tyr residue.

Example 8 Synthesis of a Cysteine Protease Inhibitor with a y-aminocarboxylate as the EWG.

Synthesis of (S)-4-(4-morpholinecarbonylphenylalanyl)amino-6-phenylhexanoic acid, Mu-Phe-Hph-y-

CO

2 H. To a solution of Mu-Phe-Hph-y-CO 2 Et, prepared according to the procedure described in Example 1 (0.5g, 1.06 mmole) was added aqueous NaOH (1 mL of a 2M solution). After 4 hr the reaction was complete. 1M HCI (4mL) was added along with water (10 mL). The product was extracted with CH 2

CI

2 (2 x 10 mL), THF (15dried over MgSO4. the solvent was removed under reduced pressure, and the residue, Mu-Phe-Hph-y-CO 2 H, was pumped to a solid Yield 0.30g Example 9 Synthesis of a Cysteine Protease Inhibitor with a y-aminophosphonate as the EWG.

I

WO 96/30353 PCT/US96/03844 47 Synthesis of diethyl (S)-4-(4-morpholinecarbonyl-phenylalanyl)amino-6-phenylhexanephosphonate (Mu-Phe-Hph-y-SO 2 Ph) was as follows. To a solution of tetraethyl methylenediphosphonate (2.00 g, 6.94 mmol) in THF (30 mL) was added sodium hydride (0.278 g of a 60% mineral oil dispersion, 6.94 mmol). The mixture effervesced rapidly and then clarified. After 5 minutes, a solution of Boc-HphH (1.83 g, 6.94 mmol) in THF (5 mL) was added. The mixture was stirred for 1 hour. 1M HCI (20 mL) was added. The product was extracted into ethyl acetate (50 mL), washed with saturated aqueous NaHCO 3 (20 mL), brine (10 mL), dried over MgSO 4 filtered, and evaporated to dryness, giving 2.46 g of intermediate, diethyl butoxycarbonylamino-6-phenyl-2-hexenephosphonate.

To a solution of this material in CH 2

CI

2 (3 mL) was added 10 mL of a 4.0 M solution of HCI in dioxane.

The mixture was stirred at room temperature for 1.5 hours. The solvents were removed under reduced pressure and the residue was dissolved in methanol (10 mL). The solution was poured into ether (400 mL). The precipitate was collected on a Buchner funnel, washed with ether (2x20 mL), and was pumped dry to give 1.25 g of intermediate, diethyl (S)-(E)-4-amino-6phenyl-2-hexenephosphonate hydrochloride. To a solution of Mu-PheOH (1.04 g, 3.74 mmol) in THF mL) at -10°C was added 4-methylmorpholine (0.412 mL, 3.74 mmol), followed by isobutyl chloroformate (0.486 mL, 3.74 mmol). The mixed anhydride was stirred for 5 minutes, whereupon a solution of (S)-(E)-4-amino-6-phenyl-2-hexene-phosphonate hydrochloride (1.25 g, 3.74 mmol) in DMF mL) was added, followed by 4-methylmorpholine (0.412 mL, 3.74 mmol). The mixture was stirred for 1 hour. Ethyl acetate (50 mL) was added. The solution was washed with 1M HCI (25 mL), saturated aqueous NaHCO 3 (25 mL), and brine (10 mL), dried over MgSO 4 filtered, and evaporated to dryness. The product, upon treatment with CH 2

CI

2 /ether/hexane (315 mL in a 15:200:100 ratio) formed an oil that solidified on drying in vacuo to give 1.44 g of diethyl (E)-4-(4-morpholinecarbonyl-phenylalanyl)-amino-6-phenyl-2-hexenephosphonate. 0.85 g of this material was dissolved in ethanol (10 mL) and was transferred to a Parr bottle charged with palladium on active charcoal. The solution was reduced on a Parr hydrogenator for 36 hours. The solution was then filtered through Celite, and the solvent was removed under reduced pressure to give 0.66 g of the final product as an oil. TLC: MeOH/CH 2

CI

2 Rf 0.27.

Example Synthesis of a Cysteine Protease Inhibitor with a y-aminoamide as the EWG.

Synthesis of benzyl (S)-3-(4-morpholinecarbonylphenyl-alanyl)-amino-6-phenylhexanamide (Mu-Phe- Hph-y-AMBzl). The Wadsworth-Emmons reagent diethyl benzylamido-carbonylmethylenephosphonate was synthesized in two steps, first by saponification of triethyl phosphonoacetate to diethyl phosphonoacetic acid, which then was dissolved in ethyl acetate to a 0.2 M concentration, treated with an equivalent of benzylamine, 0.1 equivalents of 4-dimethylamino-pyridine, and one equivalent of dicyclohexyl-carbodiimide. To a solution of this Wadsworth-Emmons reagent (2.59 g, 9.08 mmol) in WO 96/30353 PCTfUS96/03844 48 THF (40 mL) at 0 C was added sodium hydride (0.363 g of a 60% mineral oil dispersion, 9.08 mmol).

The mixture was stirred at room temperature for 15 minutes, whereupon a solution of Bochomophenylalaninal (2.39 g, 9.08 mmol) in THF (10 mL) was added. The mixture was stirred for 1 hour. 1M HCI (30 mL) was added. The product was extracted into ethyl acetate (100 mL), washed with saturated aqueous sodium bicarbonate (50 mL), brine (30 mL), dried over MgSO 4 filtered, concentrated, and crystallized from ether/hexane to give 1.81 g of benzyl tertbutoxycarbonylamino-6-phenyl-2-hexenamide. This material was dissolved in CH 2

CI

2 (5 mL). To the solution was added HCI/dioxane (10 mL of a 4.0M solution). The mixture was stirred for 3 hours at room temperature. The solvents were removed under reduced pressure. The residue was dissolved in methanol (5 mL) and poured into ether (300 mL), whereupon the intermediate, benzyl amino-6-phenyl-2-hexenamide hydrochloride, separated out as an oil, in 82% yield (1.25 To a solution of Mu-PheOH (1.05 g, 3.78 mmol) in THF (15 mL) at -10°C were added 4-methylmorpholine (0.416 mL 3.78 mmol) and isobutyl chloroformate (0.490 mL, 3.78 mmol). The mixture was stirred for minutes, whereupon a solution of benzyl (S)-(E)-3-amino-6-phenyl-2-hexenamide hydrochloride (1.25 g, 3.78 mmol) in THF (3 mL) was added, followed by 4-methylmorpholine (0.416 mL, 3.78 mmol). The mixture was stirred for 45 minutes. Ethyl acetate (40 mL) was added. The solution was washed with 1M HCI (10 mL), saturated aqueous sodium bicarbonate (10 mL), brine (5 mL), dried over MgSO 4 filtered, and evaporated to dryness. The intermediate, benzyl morpholinecarbonyl-phenylalanyl)amino-6-phenyl-2-hexenamide, was precipitated from CH 2

CI

2 /ether in 56% yield. 0.48 g (0.865 mmol) of this material was dissolved in ethanol (10 mL) and transferred to a Parr bottle charged with 5% palladium on active carbon. The mixture was reduced on a Parr hydrogenator for 4 hours. The solution was filtered through Celite, and the solvent was removed under reduced pressure. The final product (Mu-Phe-Hph-y-AMBzl) was crystallized from ethanol/hexane, giving 0.25 g TLC: (50% ethyl acetate/hexane) R, 0.45.

Example 11 Synthesis of a Cysteine Protease Inhibitor with a y-aminoamide as the EWG.

Synthesis of phenyl (S)-3-(4-morpholinecarbonylphenyl-alanyl)-amino-6-phenylhexanamide (Mu-Phe- Hph-y-AMPh). To a solution of Mu-Phe-Hph-y-CO 2 H, (0.30g, as prepared according to Example in THF (5 mL) at -10°C was added triethylamine (90 1 eq.) followed by addition of isobutyl chloroformate (0.083 mL, 1 After 5 min, aniline (0.058 mL) was added. The cooling bath was removed and the reaction stirred at room temp for 2 hr. CH 2

CI

2 (30 mL) was added. The solution was washed with 1M HCI and saturated aqueous sodium bicarbonate (10 mL each), dried over MgSO 4 filtered, and the solvent was removed under reduced pressure. The residue was triturated with Et 2

O,

filtered, and dried in vacuo to give 0.29 g of the product, Mu-Phe-Hph-y-AMPh. TLC MeOH/CH 2

CI

2 R, 0.70, strongly absorbs UV (254 nm), 12.

WO 96/30353 PCT/US96/03844 49 Example 12 Synthesis of a Cysteine Protease Inhibitor with a y-aromatic as the EWG.

Synthesis of (S)-4-aminophenyl-3-(4-morpholine-carbonylphenylalanyl)amino-5-phenylpentane hydrochloride, (Mu-Phe-hPhe-y-C 6

H

4

NH

2

.HCI).

Triphenylphosphine (38.17 g, 0.146 mole) and 4-nitrobenzyl chloride (25g, 0.146 mole) were dissolved in CH 3 CN (100 mL) and heated at reflux for 2 hours, and then allowed to cool to room temperature. The reaction mixture was diluted with Et20 (300 mL), the white solid was filtered, washed with Et2O (200 mL), and dried in vacuo, giving 53.3 g of 4nitrobenzyltriphenylphosphonium chloride as a single spot on TLC: (Rf=0.71, 4:1:1 butanol:acetic acid:water). 1 H-NMR (d 6 -DMSO): 5.40-5.50 (2H, d, CH 2 P, J=20Hz); 7.20-7.40 (2H, dd, aromatic); 7.40-7.80 (12H, m, aromatic); 7.90-8.00 (3H, m, aromatic); 8.10-8.20 (2H, d, aromatic).

To a stirred suspension of 4-nitrobenzyltriphenylphosphonium chloride (10.02 g, 23.1 mmol) in

CH

2

CI

2 (100 mL) was added 4-methylmorpholine (2.54 mL, 23.1 mmol) was added. When all the solid had dissolved, Boc-HphH (4.04 g, 15.4 mmol) was added. After 24 hrs., the reaction mixture was diluted with CH 2

CI

2 (200 mL), and filtered. The filtrate was washed with 1M HCI (200 mL) saturated aqueous sodium bicarbonate (200 mL); dried over MgSO 4 filtered and concentrated under reduced pressure, giving 4.00 g of crude intermediate, a portion of which was purified by chromatography (gradient elution: 10-30% ethyl acetate/hexane) to permit NMR analysis of the intermediate, (S)-t-butoxycarbonyl-3-amino-1-(4-nitrophenyl)-5-phenyl-1-pentene.

TLC: (30% EtOAc /hexane) R,=0.4 9 To a solution of this material (2.76 g, 7.2 mmol) in Et2O mL), was added a solution of anhydrous p-toluenesulfonic acid (2.76 g, 16.0 mmol) in Et2O mL). The reaction was left to stir 16 hrs, filtered; washed solid with Et 2 O (25 mL), and dried in vacuo, giving 2 g of (S)-3-amino-1-(4-nitrophenyl)-5-phenyl-1-pentene as a single spot on TLC: (Rf=0.49, 10% MeOH/CH 2

CI

2 To a solution of Mu-PheOH (1.29 g, 4.63 mmol) in THF (20 mL) were added 4-methylmorpholine (0.51 mL, 4.63 mmol) and isobutyl chloroformate (0.61 mL, 4.63 mmol). After 3 minutes, a solution of 3-amino-l-(4-nitrophenyl)-5-phenyl-1-pentene hydrochloride, prepared by HCI/dioxane-mediated deprotection of 3-tert-butoxycarbonylamino-1-(4-nitrophenyl)-5phenyl-1-pentene precursor, 1.34 g, 4.20 mmol) in CH 2

CI

2 (20 mL), followed by 4methylmorpholine (0.51 mL, 4.63 mmol). The mixture was stirred overnight while warming to room temperature. The solution mixture was diluted with CH 2

CI

2 (100 mL), washed with 1M HCI (200 mL), saturated aqueous sodium bicarbonate (200 mL); dried over MgSO,, filtered, and

I

WO 96/30353 PCTIUS96/03844 concentrated under reduced pressure to give a yellow oil. This material was crystallized from CHClI 2 /ether (2:100, 20 mL) to give 1.00 g of as an approximately 4:1 E/Z mixture. 0.27 g (0.49 mmol) of this material was dissolved in ethanol mL), transferred to a Parr bottle charged with 5% palladium on carbon (0.10 g) and reduced on a Parr hydrogenator for 8 hours/ The mixture was filtered and the solvent was removed under reduced pressure. The residue was dissolved in in 4:1 ether/CH 2

CI

2 (100 mL), to which HCI/dioxane (0.136 mL of a 4.0 M solution) was added. The product, Mu-Phe-Hph-y-

CH

4

NH

2 .HCI, was filtered and dried in vacuo. Yield 0.15 g TLC: methanol/CH 2

C

2 0.31.

Example 13 Synthesis of a Cysteine Protease Inhibitor with a P-aminosulfone as the EWG.

Synthesis of (S)-2-(4-morpholinecarbonylphenyl-alanyl)amino-4- phenyl--phenylsulfonylbutane (Mu-Phe-Hph-P-SO 2 Ph). Preparation of Boc-homophenylalaninol (Boc-Hph-P-OH) and tert-butoxycarbonylamino-1-methanesulfonyloxy-1-phenylbutane (Boc-Hph-P-OMs or Bochomophenylalaninol mesylate) followed a similar scheme to that reported by Spaltenstein, Carpino, Miyake, and Hopkins, above. To a solution of Boc-homophenylalanine (10.29 g, 36.84 mmol) in THF (100 mL) at -10 0 C were added 4-methylmorpholine (4.05 mL, 36.84 mmol) and isobutyl chloroformate (4.78 mL, 36.84 mmol). The solution was stirred for 10 minutes, and then was filtered. The filtrate was carefully added to a stirred solution of sodium borohydride (2.77 g, 73.67 mmol) in water (100 mL) at 0°C. The mixture was stirred for 30 minutes. Saturated aqueous sodium bicarbonate (200 mL) was added. The product was extracted with CH 2

CI

2 (2x100 mL), dried over MgSO 4 filtered, and the solvent was removed under reduced pressure to give 9.78 g (100%) Boc-homophenyl-alaninol. TLC: (30% ethyl acetate/hexane) Rf 0.15. 5.83 g (21.97 mmol) of this material was dissolved in CH 2

CI

2 (150 mL), cooled to 0 C, and treated with methanesulfonyl chloride (4.15 mL, 53.71 mmol), and triethylamine (9.24 mL, 66.3 mmol). The mixture was stirred for 30 minutes. Water (100 mL) was added; the mixture was stirred vigorously. The organic phase was separated, dried over MgSO 4 filtered, and the solvent was removed under reduced pressure, giving 7.31 g yield. TLC: (30% ethyl acetate/hexane) R, 0.21. A similar procedure was employed to prepare the corresponding benzenesulfonate ester of Boc-Hph-P-OH.

To a solution of thiophenol (0.653 mL, 6.36 mmol) in THF (5 mL) was added sodium hydride (0.254 g, 6.36 mmol as a 60% mineral oil dispersion. The mixture was stirred for 10 minutes. A solution of Boc-homophenylalaninol benzenesulfonate (2.58 g, 6.36 mmol) in THF (5 mL) was

I_

WO 96/30353 PCT/US96/03844 51 added. The solution was stirred at room temperature for 10 minutes. Methanol (2 mL) was then added, and the mixture was heated at reflux for 1 hour. The solution was cooled, diluted with 1M NaOH (25 mL), extracted with CH 2

CI

2 (100 mL), dried over MgSO 4 filtered, and the solvent was removed under reduced pressure. The residue was dissolved in CH 2

CI

2 (35 mL) and cooled to 0°C. To the solution was added 4-chloroperbenzoic acid (3.71 g, 13.99 mmol, estimated peracid content 65% by weight). The mixture was stirred for 1 hour, whereupon 10% NaOH (35 mL) and saturated aqueous NaHSO 3 (35 mL) were added. The mixture was extracted with CH 2

CI

2 (3x50 mL portions), dried over MgSO 4 filtered, and the solvent was removed under reduced pressure to give a waxy solid, (S)-2-tert-butoxycarbonylamino-4-phenyl-1-phenylsulfonylbutane.

TLC:

ethyl acetate/hexane) Rf 0.32. 1.25 g of this material was dissolved in CH 2

CI

2 (5 mL) and treated with HCI/dioxane (5 mL of a 4.0M solution). The mixture was stirred for 2 hours at room temperature. The solution was poured into ether (200 mL), forming an oily residue. The supernatant was discarded. The residue was again dissolved in CH 2 CI, (10 mL), and poured into ether (200 mL). The intermediate, (S)-2-amino-4-phenyl-1-phenylsulfonylbutane hydrochloride precipitated out. The solid was filtered and dried in vacuo to give 0.40 g of material (38% yield from Boc-homophenylalaninol benzenesulfonate.

To a solution of Mu-PheOH (0.342 g, 1.23 mmol) in THF (10 mL) at -100C were added 4methylmorpholine (0.135 mL, 1.23 mmol) and isobutyl chloroformate (0.159 mL, 1.23 mmol).

The mixture was stirred for 10 minutes, whereupon (S)-2-amino-4-phenyl-1-phenylsulfonylbutane hydrochloride (0.40 g, 1.23 mmol) was added, followed by 4-methylmorpholine (0.135 mL, 1.23 mmol). The mixture was stirred for 45 minutes. 1M HCI (15 mL) was added. The product was extracted with ethyl acetate (30 mL), washed with saturated aqueous sodium bicarbonate mL), brine (15 mL), dried over MgSO 4 filtered, and the solvent was removed under reduced pressure. The final product, Mu-Phe-Hph-p-SOPh, weighed 0.68 g (100% yield).

Example 14 Synthesis of a Cysteine Protease Inhibitor with a 1-aminosulfone as the EWG.

Synthesis of (S)-2-tert-butoxycarbonylamino-4-phenyl--(1 '-trimethylsilylethyl)-sulfonylbutane (Boc-Hph-p-SO 2

CH

2

CH

2 TMS). To a solution of 2-trimethylsilylethanethiol (0.86 g, 6.41 mmol), synthesis described by Anderson, Ranasinghe, Palmer, and Fuchs, above) in THF (10 mL) was added sodium hydride (0.256 g, 6.41 mmol as a 60% mineral oil dispersion). The mixture was stirred for 10 minutes. Boc-homophenylalaninol mesylate (2.00 g, 5.82 mmol, synthesis described in Example 13, above) was added. The solution was stirred for 2 hours. Ethyl acetate mL) was added. The solution was washed with 30 mL each of 1M HCI, saturated aqueous sodium bicarbonate, and brine, dried over MgSO 4 filtered, and the solvent was removed under

I

WO 96/30353 PCT/US96/03844 52 reduced pressure, giving the intermediate (S)-2-tert-butoxycarbonylamino-4-phenylbutyl trimethylsilylethyl sulfide. TLC: ethyl acetate/hexane) Rf 0.22. This material was dissolved in CH 2

CI

2 (50 mL), cooled to -10 0 C, and treated with 4-chloroperbenzoic acid (3.24 g, 12.22 mmol, estimated 65% peracid content). The mixture was stirred overnight. The suspension was filtered, and saturated aqueous NaHSO 3 (40 mL) and saturated aqueous sodium bicarbonate (50 mL) were carefully added to the filtrate. The organic phase was separated, dried over MgSO 4 filtered, and the solvent was removed under reduced pressure to give the product, Boc-Hph--SO 2

CHCH

2 TMS in quantitative mass recovery from the mesylate.

TLC: (30% ethyl acetatelhexane) Rf 0.49.

Example Synthesis of a Cysteine Protease Inhibitor with a p-aminosulfone as the EWG.

Synthesis of (S)-2-(4-morpholinecarbonylphenylalanyl)-amino- -chloromethylsulfonyl-4phenylbutane (Mu-Phe-Hph-P-SO 2

CH

2 CI. To a solution of Boc-Hph-P-SO 2

CH

2

CH

2 TMS (0.90 g, 2.18 mmol as described in Example 14) in THF (2 mL) were added tetrabutylammonium fluoride (8.7 mL of a 1.OM THF solution) and several molecular sieves. The mixture was stirred overnight at room temperature. Bromochloromethane (5 mL) was added. The mixture was heated at reflux for 1 hour, cooled, and the volatile components were removed under reduced pressure.

The residue was dissolved in ethyl acetate (75 mL), washed with 1M HCI (50 mL), dried over MgSO,, filtered, and the solvent was removed under reduced pressure. The residue, crude 2-tert-butoxycarbonylamino-1-chloromethylsulfonyl-4-phenylbutane, was dissolved in ether (3 mL). A solution of anhydrous 4-toluenesulfonic acid (0.80 g, 4.70 mmol) in ether (3 mL) was added. The mixture was stirred at room temperature overnight. Ether (100 mL) was added.

The solid intermediate, (S)-2-amino-1-chloromethyl-sulfonyl-4-phenylbutane 4-toluenesulfonate (TsOH.Hph-P-SO 2

CH

2 CI), was filtered, the solids were washed with ether (2x20 mL), and dried in vacuo to give 0.193 g of material (24% from Boc-Hph-P-SOCH 2

CH

2

TMS).

To a solution of Mu-PheOH (0.109 g, 0.392 mmol) in THF (3 mL) at -10 0 C were added 4methylmorpholine (43 uL, 0.392 mmol) and isobutyl chloroformate (51 pL, 0.392 mmol). The mixture was stirred for 10 minutes, whereupon TsOH.Hph-P-SO 2

CH

2 CI (0.17 g, 0.392 mmol) was added, followed by 4-methylmorpholine (43 pL, 0.392 mmol). The mixture was stirred for minutes. Ethyl acetate (20 mL) was added. The solution was washed with 1M HCI, saturated aqueous sodium bicarbonate, and brine (2 mL each) dried over MgSO 4 filtered, and the solvent was removed under reduced pressure, to give the final product, Mu-Phe-Hph-P-SO 2

CH

2 CI mg, 48% yield.

WO 96/30353 PCTIUS96/03844 53 Example 16 Synthesis of a Cysteine Protease Inhibitor with an a-aminosulfone as the EWG.

Synthesis of 1-(tert-butoxycarbonyl)amino-2-methyl- -phenylsulfonylpropane (Boc-Val-a-

SO

2 Ph). To a stirred suspensionof t-butylcarbamate (2.34 g, 20 mmol) and sodium benzenesulfinate (3.28 g, 20 mmol) in water (20 mL) was added a solution of isobutyraldehyde (2.00 mL, 22 mmol) in formic acid (5 mL). The mixture was stirred at room temperature overnight. The precipitate was filtered, washed with water (2x50 mL) and crystallized from isopropanol/water to give 4.72 g of the product.

Example 17 Synthesis of a Cysteine Protease Inhibitor with an a-aminosulfone as the EWG.

Synthesis of 1 -benzyloxycarbonylamino-3-phenyl-1-phenylsulfonylpropane (Z-Hph-a-SO 2 Ph).

To a suspension of sodium benzenesulfinate (10 g, 60.9 mmol) and benzyl carbamate (9.21 g, 60.9 mmol) in water (40 mL) was added hydrocinnamaldehyde (8.8 mL, 67 mmol) in formic acid mL). The mixture was heated at 70 0 C for 1 hour, then permitted to cool to room temperature overnight. The product crystallized out; it was filtered and recrystallized from hot isopropanol, giving 23 g (100%) yield. TLC: (30% ethyl acetate/hexane) Rf 0.37.

Example 18 Synthesis of a Cysteine Protease Inhibitor with an a-aminosulfone as the EWG.

Synthesis of (R)-1-(4-morpholinecarbonylphenylalanyl)amino-3- phenyphenylsulfonylpropane and (S)-l-(4-morpholinecarbonylphenylalanyl)amino-3-phenyl-1-phenylsulfonylpropane (Mu- Phe-Hph-a-SO 2 Ph, epimers separated). Method A: Z-Hph-a-SO 2 Ph (1.0 g, 2.44 mmol) was treated with 30% hydrogen bromide in acetic acid (5 mL). After 30 minutes, the mixture was diluted with ether (300 mL), filtered, washed with ether (2x30 mL), and dried in vacuo to give 0.74 g 1-amino-3-phenyl-1-phenylsulfonylpropane hydrobromide (HBr.Hph-a-SO 2 Ph). To a solution of Mu-PheOH (0.64 g, 2.3 mmol) in THF (15 mL) were added 4-methylmorpholine (0.302 mL, 2.3 mmol) and isobutyl chloroformate (0.312 mL, 2.3 mmol). The mixture was stirred for 10 minutes. HBr.Hph-a-SOPh (0.74 g, 2.1 mmol) was added, followed by 4methylmorpholine (0.302 mL, 2.3 mmol). After 45 minutes, the mixture was diluted with ethyl acetate (30 mL), washed with 15 mL each of 1M HCI, saturated aqueous sodium bicarbonate, and brine, dried over MgSO,, filtered, and the solvent was removed under reduced pressure to give 0.75 g of the product, Mu-Phe-Hph-a-SO2 Ph.

WO 96/30353 PCTJUS96/03844 54 Method B: To a solution of phenylalanine amide hydrochloride (10 g, 50 mmol) in DMF (50 mL) and CH 2

CI

2 (50 mL) were added triethylamine (13.9 mL, 100 mmol) and 4-morpholinecarbonyl chloride (5.9 mL, 50 mmol). The mixture was stirred overnight. The solvents were removed under reduced pressure. The residue was dissolved in ethyl acetate (50 mL), and filtered. Ether was added to the filtrate until the solution became turbid. 7.2 g (80% yield) of the intermediate, 4-morpholinecarbonylphenylalanine amide (Mu-Phe-NH 2 crystallized from the solution after 3 days. To a solution of Mu-PheNH 2 (2.24 g, 8.1 mmol) in formic acid (5 mL) was added, with stirring, hydrocinnamaldehyde (1.17 mL, 8.9 mmol). The mixture was stirred for 5 hours, whereupon sodium benzenesulfinate (1.33 g, 8.1 mmol) was added. The mixture was quickly heated to reflux over a five minute period, and was allowed to cool to room temperature. The solution was then permitted to stir for three days. An equal volume of water was added. The product was extracted with CH 2

CI

2 (3x100 mL), dried over MgSO 4 filtered, and the solvent was removed under reduced pressure. The yield of product, diastereomeric and morpholine-carbonylphenylalanyl)amino-3-phhenylsulfonyl--phenyl-propane, was 3.9 g TLC (50% ethyl acetate/CH 2

CI

2 R, 0.27,0.34.

The diastereomers were separated by flash chromatography on 230-400 mesh silica gel ethyl acetate/CH 2

CI

2 gradient elution).

Example 19 Inhibition of Cysteine Proteases with the Inhibitors of the Invention Conditions for cathepsin B: 50 mM phosphate, pH 6.0, 2.5 mM EDTA, 2.5 mM DTT. substrate: [Z-Arg-Arg-AMC] 50 mM (Km 190 mM). The assay at 25° was started by the addition of cat B (final concentration approx 10 nM) and the increase in fluorescence at 450 nm with excitation at 380 nm was followed over 2 min. The depression in the rate of substrate hydrolysis following addition of varying concentrations of inhibitors was noted. The assay was linear throughout the range observed. Duplicate runs were measured.

Conditions for cathepsin L: 50 mM acetate, pH 5.5, 2.5 mM EDTA, 2.5 mM DTT. substrate: [Z-Phe-Arg-AMC] 5 mM (Km 2 mM). The assay at 25 0 was started by the addition of cat L (final concentration approx 1 nM) and the increase in fluorescence at 450 nm with excitation at 380 nm was followed over 2 min. The depression in the rate of substrate hydrolysis following addition of varying concentrations of inhibitors was noted. The assay was linear throughout the range observed. Duplicate runs were measured.

WO 96/30353 PCTJUS96/03844 Conditions for cathepsin S: 50 mM phosphate, pH 6.5, 2.5 mM EDTA, 2.5 mM OTT. substrate: [Z-Val-Val-Arg-AMC] 10 mM (Km 18 mM). The assay at 250 was started by the addition of cat S (final concentration approx 30 pM) and the increase in fluorescence at 450 nm with excitation at 380 nm was followed over 2 min. The depression in the rate of substrate hydrolysis following addition of varying concentrations of inhibitors was noted. The assay was linear throughout the range observed. Duplicate runs were measured.

Conditions for cruzain were the same as for cathepsin L with the exception that the Km for the substrate was 1 mM.

The respective K, values were estimated by using the Dixon plot as described by Irwin Segel in Enzyme Kinetics: Behavior and analysis of rapid equilibrium and steady-state enzyme systems, 1975, Wiley-lnterscience Publication, John Wiley Sons, New York.

The results are shown in Table 2.

Table 2 Inhibitor cathepsin B cathepsin L fcathepsin S cruzain (KI pM) I I I_ Mu-Phe-(DL)HphaSO 2 Ph 3,000 13 5 1 Mu-Phe-HphaSO 2 Ph 2.6 Mu-Phe-(DL)HphaSO 2 Ph, 3.7 Mu-Leu-HphaSO 2 Ph 16 1.3 1.6 0.27 Mu-Leu-HphaSO 2 Bzl 54 0.60 4.2 0.76 Mu-Phe-HphaSO 2

CH

2 F 170 1.5 2.8 Mu-Phe-HphaSO 2 Bzl 77 1.2 5.2 0.92 Mu-Phe-HphaSO 2

CR

3 50 0.18 2.2 0.23 Mu-Phe-HphI3SO 2 Ph 1,100 29 0.94 5.7 Mu-Phe-HphySO 2 Ph 48 10 0.16 4.3 Phac-Phe-HphySO 2 Ph >>1O 0.41 12.5 1.8 Mu-Np2-HphySO 2 2Np 20 0.26 0.53 0.10 Mu-Phe-HphySO 2 EtPh 190 0.17 0.082 5.9 Suc-Phe-HphySO 2 Ph >1000 1.0 0.07 MeOSuc-Phe-HphySO 2 Ph 81 3.2 1.2 4.7 Suc-Np2-HphySO 2 Ph >1000 2.3 0.50_ 0.78 Suc-Np2-HphySO,2Np >1000 0.11 0.24 10.23 WO 96/30353 PCTIUS96/03844 Z-0-Ala-Phe-HphvSO 2 Ph 52 0.79 3.0 0.54 0-Ala-Phe-HphVS0 2 Ph >>50 14 11 14 Mu-Tyr-HphvSO 2 Ph 2.3 9.5 Mu-Phe-HphyCO 2 Et 1.6 0.48 0.19 0.91 Mu-Phe-HphyCONHPh 2.6 2.0 1.3 0.13 Mu-Phe-HphyCONHBzI >>50 19 30 7.7 Mu-Phe-HphyPO(O 2 Et) 2 17 3.0 1.4 Mu-Phe-Hph-yPh-OMe 4.8 0.94 0.37 0.89 Mu-Phe-Hph-yPh-NH 2 >>50 2.9 9.1 EXAMPLE The following are representative phamnaceutical formulation containing a cysteine protease inhibitor of this invention.

ORAL FORMULATION A representative solution for oral administration contains: Cysteine protease inhibitor Citric Acid Monohydrate Sodium Hydroxide Flavoring Water 100 to 1000 mg 105 mg 18 mg q.s. to 100 mL INTRAVENOUS FORMULATION A representative solution for intravenous adminstration contains: Cysteine protease inhibitor Dextrose Monohydrate Citric Acid Monohydrate Sodium Hydroxide Saline for Injection 10 to 100 mg q.s. to make isotonic 1.05 mg 0.18 mg q.s. to 1.0 ml- TABLET FORMULATION r A representative tablet form may contain: Cysteine protease inhibitor 1% Microcrystalline Cellulose 73% Stearic Acid Colloidal Silica 1% Throughout this specification and the claims which follow, unless the context requires otherwise, the word "comprise", and variations such as "comprises" and "comprising", will be understood to imply the inclusion of a stated integer or step or group of integers or steps but not the exclusion of any other integer or step or group of integers or steps.

*o a a o

Claims

1. A cysteine protease inhibitor of Formula I: A B Z A BX S(O)R2 I in which: n is 0 to 13; A-B represents a linkage selected from -C(O)NR 3 -CH 2 NR 3 -C(O)CH 2 and -NR 3 wherein R 3 is hydrogen or as defined below; X represents a bond, methylene or the linkage -CH 2 CH(R 4 wherein R4 is hydrogen, alkyl or arylalkyl; Y is -CH(RS)- or -N(R 5 wherein R 5 is hydrogen or as defined below; Z is -(CH 2 2 -C(R 6 )(R 7 or -N(R 7 wherein R 6 is hydrogen or methyl and R 7 is as defined below; Z is -(CH2) 2 -C(R 6 )(R 8 or -N(R 8 wherein R 6 is hydrogen or methyl and R 8 is as defined below; R 1 is hydrogen, alkyloxycarbonylalkanoyl, alkyloxycarbonyl, alkanoyl (optionally substituted with a radical selected from carboxy, alkyloxycarbonyl and heterocycloalkylalkanoylamino), cycloalkylcarbonyl, heterocycloalkylcarbonyl (optionally substituted with a radical selected from hydroxy, alkyl, alkanoyl, alkyloxycarbonyl, *"*arylalkyloxycarbonyl and heterocycloalkylcarbonyl), arylalkyloxycarbonyl, carbamoyl, 25 alkylcarbamoyl, dialkylcarbamoyl, arylcarbamoyl, arylalkylcarbamoyl, arylalkanoyl, aroyl, alkylsulfonyl, dialkylaminosulfonyl, arylsulfonyl or heteroarylsulfonyl; R 7 and R8 are independently hydrogen, alkyl (optionally substituted with a radical selected from hydroxy, amino, alkylamino, dialkylamino, uriedo, mercapto, alkylthio, carboxy, carbamoyl, alkylcarbamoyl, dialkylcarbamoyl, alkylsulfonyl and guanidino, or a protected derivative thereof), cycloalkyl, cycloalkylalkyl, heteroaryl, heteroarylalkyl, a group 4j RA, selected from aryl and arylalkyl (which group is optionally substituted at its aryl ring with P:\OPER\DCD\53674-96.215 3/8/99 59 one to three radicals selected from hydroxy, amino, guanidino, halo, optionally halo-substituted alkyl, alkyloxy and aryl, or a protected derivative thereof) or together with an adjacent R 3 or R 5 forms a divalent radical selected from (C 3 4 )methylene and 1 ,2-phenylenedimethylene (which radical is optionally substituted with hydroxy, or a protected derivative thereof, or oxo); and R 2 is hydrogen, alkyl (optionally substituted with one or more radicals selected from amino, guanidino, halo, hydroxy, alkyloxy, nitro, alkylsulfonyl and arylsulfonyl, or a protected derivative thereof), cycloalkyl, cycloalkylalkyl or a group selected from aryl and arylalkyl (which group is optionally substituted at its aryl. ring with one to two radicals selected from amino, halo, hydroxy, optionally halo-substituted alkyl, alkyloxy, nitro, alkylsulfonyl and arylsulfonyl, or a protected derivative thereof); and the pharmaceutically acceptable salts, individual isomers and mixtures of isomers thereof.

2. The cysteine protease inhibitor of Claim I wherein the dissociation constant for inhibition of a protease with said inhibitor is no greater than about 100 i iM. 0%3. The cysteine protease inhibitor of Claim 1 in which n is 0 to 5; A-B represents a linkage selected from -C(O)NR 3 Y is -N(R 5 Z is -(CH 2 2 or -C(R 6 )(R 7 Z' is -CH(R 8 R 1 is hydrogen, alkyloxycarbonylalkanoyl of overall 3 to 10 carbon atoms, (C 1 9 )alkoxycarbonyl, (C 2 1 )alkanoyl (optionally substituted with a radical selected from carboxy, (C I 9 )alkyloxycarbonyl and hetero(C 4 8 )cycloalkyl(C 2 1 )alkanoylamino), (C 4 9 )cycloalkylcarbonyl, hetero(C 4 8 )cycloalkylcarbonyl (optionally substituted with a radical selected from hydroxy, (C 1 5 )alkyl, (C 1 5 )alkanoyl, (CI- 5 )alkloxycarbonyl, (C 6 I 10 )aryl(C 1 5 )alkyloxycarbonyl and hetero(C 4 8 )cycloalkylcarbonyl), :25 (C 6 1 )aryl(C 1 I 5 )akyoxycarbonyl, carbamoyl, (C 1 5 )alkylcarbamnoyl, di(C 1 5 )alkylcarbamoyl, (C 6 -I)arylcarbamoyl, (C 610 )aryl(C 1 5 )alkylcarbamnoyl, (C 610 )aryl(C 15 )alkanoyl, (C 7 1 1 )aroyl, (C 1 5 )alkylsulfonyl, di(C 1 5 )alkylaminosulfonyl, (C 6 1 0 )arylsulfonyl or hetero(C 5 8 )arylsulfonyl; R 8 and R 7 are independently (C 3 7 )cycloalkyl, (C 3 7 )cycloalkyl(C 1 5 )alkyl, pyridyl, thienyl, furyl, imidazolyl, indolyl, pyridyl(C 1 6 )alkyl, thienyl(CI-. 6 )alkyl, fuiryl(C 1 6 )alkyl, imidazolyl(C 1 6 )alkyl, indolyl(CI-. 6 )alkyl, (C 1 5 )alkyl, ~.(which group is optionally substituted with a radical selected from mercapto, carboxy, P:\OPER\DCD\53674-96.213 3/8/99 S- amino, methylthio, methylsulfonyl, carbamoyl, dimethylcarbamnoyl, guanidino and hydroxy, or a protected derivative thereof), a group selected from phenyl, naphthyl, phenyl(C 1 6 )alkyl, naphthyl(C 1 6 )alkyl, (which group is optionally substituted at its aryl ring with one to three radicals selected from amino, hydroxy, chioro, bromo, fluoro, methyl, trifluoromethyl, methoxy and phenyl, or a protected derivative thereof) or together with an adjacent R 3 or R forms a divalent radical selected from (C 3 4 )methylene and 1 ,2-phenylenedimethylene (which radical is optionally substituted with hydroxy, or a protected derivative thereof, or oxo); R 2 is (C 1 5 )alkyl (optionally substituted with one or two radicals selected from amino, chioro, bromo, fluoro, iodo, hydroxy and methoxy, or a protected derivative thereof), perhalo(C 1 5 )alkyl, (C 3 7 )cycloalkyl, (C 3 7 )cycloalkyl(C1 5 )alkyl or a group selected from phenyl, pentafluorophenyl, naphthyl and phenyl(C I -)alkyl (which group is optionally substituted at its aryl ring with one to two radicals selected from amino, chioro, bromo, fluoro, hydroxy, methoxy and optionally halo-substituted methyl, or a protected derivative thereof) and R 4 is hydrogen, (C 1 5 )alkyl or (C 6 -I 0 )aryl(C 1 5 )alkyl.

4. The cysteine protease inhibitor of Claim 3 in which n is 0 to 2; Z is -(CH 2 2 or -C(R 6 )(R 7 (with the proviso that when n is 0, Z is not -(CH 2 2 R 1 is hydrogen, V. (C 4 8 )alkoxycarbonyl, (C 2 6 )alkanoyl (optionally substituted with a radical selected from carboxy, (C I 5 )alkyloxycarbonyl and hetero(C 4 8 )cycloalkyl(C 4 6 )alkanoylamino), 0 C()N3 1 22 wherein R 21 and R 2 together form aza(C 2 6 jr-nethylene, oxa(C 2 6 )methylene a or (C 3 7 )methylene, (C 4 8 )cycloalkylcarbonyl, benzyloxycarbonyl, acetyl, benzoyl. or dimethylaminosulfonyl; R 8 and R7~ are independently (C 5 6 )cycloalkyl, a a (C 5 6 )cycloalkylmethyl, 3-pyridyl, 2-thienyl, 2-furyl, 4-imidazolyl, 3-indolyl, 3-pyridylmethyl, 2-thienylmethyl, 2-furylmethyl, 4-imidazolylmethyl, 3-indolylmethyl, (C I 5 )alkyl (optionally substituted with a radical selected from mercapto, carboxy, amino, methylthio, methylsulfonyl, carbamoyl, dimethylcarbamoyl, guanidino and hydroxy, or a protected derivative thereof), a group selected from phenyl., 1-naphthyl, 2-naphthyl, benzyl, 1-naphthylmethyl, 2-naphthylmethyl and 2-phenylethyl (which group is optionally substituted at its aryl. ring with one radical selected from hydroxy, amino, chloro, bromo and fluoro, or a protected form thereof) or together with an adjacent R 3 or Wi forms a divalent Sradical selected from (C 3 4 )methylene and 1 ,2-phenylenedimethylene (which radical is F- P:\OPER\DCD\53674-%.215 318199 -61- optionally substituted with hydroxy, or a protected derivative thereof, or oxo); R 2 is (C 1 5 )alkyl (optionally substituted with one or two radicals selected from amino, chloro, bromo, fluoro and hydroxy, or a protected derivative thereof), perfluoro(C 1 5 )alkyl, 6 )cycloalkyl, 6 )cycloalkylmethyl or a group selected from phenyl, naphthyl and benzyl (which group is optionally substituted with one radical selected from amino hydroxy, chloro, bromo or fluoro, or a protected derivative thereof) and R 4 is hydrogen or methyl. The cysteine protease inhibitor of Claim 4 in which n is 0 to 1; Z is -C(R 6 )(R 7 R 1 is hydrogen, tert-butoxycarbonyl, benzyloxycarbonyl, acetyl, 3-carboxypropionyl, 3-methoxycarbonylpropionyl, biotinylaminohexanoyl, phenylacetyl, benzoyl, dimethylaminosulfonyl, benzylsulfonyl, 1 -piperizinylcarbonyl, 4-methyl-1 -piperazinylcarbonyl or 4-morpholinylcarbonyl; R 8 is butyl, 2-phenylethyl, 2-methylsulfonylethyl, 2-tert-butoxycarbonylethyl, 2-tert-butoxycarbonylmethyl, 4-tert-butoxycarbonylaminobutyl, 4-benzoylaminobutyl or benzyloxymethyl; R 2 is methyl, trifluoromethyl, optionally substituted phenyl, 2-naphthyl or 2-phenylethyl; R 4 is hydrogen; and R 7 is 3-pyridylmethyl, 2-thienylmethyl, 2-furylmethyl, 4-imidazolylmethyl, 3-indolylmethyl, (C 1 -5)alkyl (optionally substituted with a radical selected from mercapto, carboxy, amino, methylthio, methylsulfonyl, carbamoyl, dimethylcarbamoyl, guanidino and hydroxy, or a protected derivative thereof), a group selected from benzyl, 1-naphthylmethyl, 20 2-naphthylmethyl and 2-phenylethyl (which group is optionally substituted at its aryl ring with one radical selected from hydroxy, amino, chloro, bromo and fluoro, or a protected form thereof) or together with an adjacent R 3 or R5 forms a divalent radical selected from (C 3 4 )methylene and 1,2-phenylenedimethylene (which radical is optionally substituted with hydroxy, or a protected derivative thereof, or oxo). S.

6. The cysteine protease inhibitor of Claim 5 in which n is 0; R3, R5 and R 6 are each hydrogen; R 1 is hydrogen, ter-butxoycarbonyl, benzyloxycarbonyl, biotinylaminohexanoyl, benzoyl, 1 -piperiziny-carbonyl, 4-methyl-i -piperazinylcarbonyl or 4-morpholinylcarbonyl; R 8 is butyl, 2-phenylethyl or 2-methylsulfonylethyl; R 2 is phenyl, l-naphthyl or 2-phenylethyl; and R 7 is (C 1 -5)alkyl, 2-methylsulfonylethyl, optionally substituted benzyl, 1 -naphthylmethyl, 2-naphthylmethyl, 3-pyridinylmethyl or 2-methylsulfonylethyl. P:\OPER\DCD\53674-96.215 3/8/99 62

7. The cysteine protease inhibitor of Claim 6 in which R 1 is 1 -piperizinylcarbonyl, 4-methyl-i1 -piperazincarbonyl or 4-morpholinylcarbonyl; R(8 is 2-phenylethyl; R(2 is phenyl or naphthyl; and R(7 is optionally substituted benzyl, 1-naphthylmethyl or 2-naphthylmethyl.

8. The cysteine protease inhibitor of Claim 7 in which X represents a bond, R' is 4-morpholinylcarbonyl, R 8 is 2-phenylethyl, R(2 is phenyl and R(7 is benzyl, namely N2-(4-morpholinylcarboflyl)-Nl -(3-phenyl-1 -phenylsulfonylpropyl)-L-phenylalaflinamide.

9. The cysteine protease inhibitor of Claim 7 in which X represents methylene, R(1 is 4-morpholinylcarbonyl, R 8 is 2-phenylethyl, 1(2 is phenyl and -R'7 is benzyi, namely N2-(4-morpholinylcarbonyl)-N' -phenyl- 1S-phenylsulfonylmethylpropyl)' L-phenylalaniamide. The cysteine protease inhibitor of Claim 7 in which X represents -CH 2 CH(W() wherein W( is hydrogen, R(1 is 4-morpholinylcarbonyl, R(8 is 2-phenylethyl, R(2 is 2-naphthyl and R 7 is 2-naphthylmethyl, namely N2-(4-morpholinylcarbonyl)N- {3-phenyl- 1S-[2-(2-naphthylsulfonyl)ethyl]propyl} -P-(2-naphthyl)-L-alalialide.

11. The cysteine protease inhibitor of Claim 7 in which X represents -CH 2 CH(R 4 wherein 1(4 is hydrogen, R(1 is 4-morpholinylcarbonyl, 0( is 2-phenylethyl, R 2 is phenyl and R(7 is 4-hydroxybenzyl, namely N2-(4-morpholinylcarbonyl)-N {3-phenyl- 1 S-[2-(2-naphthylsulfonyl)ethyllpropyl} -L-tyrosinamide. :12. The cysteine protease inhibitor of Claim 7 in which X represents -CH 2 CH(R 4 wherein W( is hydrogen, R(1 is 4-morpholinylcarbonyl, R(8 is 2-phenylethyl, 1(2 is phenyl and R(7 is benzyl, namely N2(-opoiycrbnl-'[-hnl 1S-(2-phenylsulfonylethyl)propylLphenylalaninamide.

13. A cysteine protease inhibitor of Formula 11: P:\OPER\DCD\53674-96.215 3/8/99 63 RI Z A Z B Z II inwhich: n is 0 to 13; A-B represents a linkage selected from -C(O)NR 3 -CH 2 NR 3 -C(O)CH 2 and -NR 3 wherein R 3 is hydrogen or as defined below; Y is -CH(R 5 or -N(R 5 wherein R 5 is hydrogen or as defined below; Z is -(CH2) 2 or wherein R' is hydrogen or methyl and K' is as defined below; Z' is -(CH 2 2 -C(R 6 or -N(R 8 wherein R 6 is hydrogen or methyl and R 8 is as defined below; R 1 is hydrogen, alkyloxycarbonylalkanoyl, alkyloxycarbonyl, alkanoyl (optionally substituted with a radical selected from carboxy, alkyloxycarbonyl and heterocycloalkylalkanoylamino), cycloalkylcarbonyl, heterocycloalkylcarbonyl (optionally substituted with a radical selected from hydroxy, alkyl, alkanoyl, alkyloxycarbonyl, arylalkyloxycarbonyl and heterocycloalkylcarbonyl), arylalkyloxycarbonyl, carbamoyl, alkylcarbamoyl, dialkylcarbamoyl, arylcarbamoyl, arylalkylcarbamoyl, arylalkanoyl, aroyl, alkylsulfonyl, dialkylaminosulfonyl, arylsulfonyl or heteroarylsulfonyl; R 7 and R0 are independently hydrogen, alkyl (optionally substituted with a radical selected from hydroxy, amino, alkylamino, dialkylamino, uriedo, mercapto, alkylthio, carboxy, carbamoyl, alkylcarbamoyl, dialkylcarbamoyl, alkylsulfonyl and guanidino, or a protected derivative thereof), cycloalkyl, cycloalkylalkyl, heteroaryl, heteroarylalkyl, a group 25 selected from aryl and arylalkyl (which group is optionally substituted at its aryl ring with one to three radicals selected from hydroxy, amino, guanidino, halo, optionally halo-substituted alkyl, alkyloxy and aryl, or a protected derivative thereof) or together with an adjacent R 3 or R forms a divalent radical selected from a divalent radical selected from (C 3 -4)methylene and 1,2-phenylenedimethylene (which radical is optionally substituted with 0 hydroxy, or a protected derivative thereof, or oxo); and R? is cyano, -C(0)OR'O, -P(0)(OR10)2, -S(0)(NR'O)Rlo, I P:\OPER\DCD\53674-96.215 3/8/99 64 -C(O)NR 1 2 -S(O) 2 NR' 2 -C(O)NHR' or -S(O) 2 NHR 1 4 wherein each R1 0 is independently hydrogen, alkyl (optionally substituted with one or more radicals selected from amino, halo, hydroxy, alkyloxy, nitro, alkylsulfonyl and arylsulfonyl, or a protected derivative thereof), cycloalkyl, cycloalkylalkyl or a group selected from aryl and arylalkyl (which group is optionally substituted at its aryl ring with one to two radicals selected from amino, halo, hydroxy, optionally halo-substituted alkyl, alkyloxy, nitro, alkylsulfonyl and arylsulfonyl, or a protected derivative thereof), R 1 1 is hydrogen, alkyl, perfluoroalkyl, cycloalkyl, cycloalkylalkyl, perfluoroaryl, perfluoroarylakyl or a group selected from aryl and arylalkyl (which group is optionally substituted at its aryl. ring with one to two radicals selected from amino, halo, hydroxy, optionally halo-substituted alkyl, alkyloxy, nitro, alkylsulfonyl and arylsulfonyl, or a protected derivative thereof), R 1 2 and R 1 3 are independently hydrogen, alkyl, cycloalkyl, cycloalkylalkyl, aryl or aralkyl and R 14 is -C(O)0R 1 0 in which R 10 is as defined above, or a group selected from Formula and 0 A( 0 (b) wherein each n, A, B, Y, Z, R' and R16 are as defined above; and the pharmaceutically acceptable salts, individual isomers and mixtures of isoifl i thereof.

14. The cysteine protease inhibitor of Claim 13 in which each n is 0 to 5; each A-B represents a linkage selected from -C(O)NR 3 each Y is -N(W 5 each Z is -(CH 2 2 or 6 )(R 7 Z' is -CH(R 8 each R' is independently hydrogen, alkyloxycarbonylalkanoyl of overall 3 to 10 carbon atoms, (C I 9 )alkoxycarbonyl, (C 2 1 )alkanoyl (optionally substituted with a radical selected from carboxy, (CI- 9 )alkyloxycarbonyl and hetero(C 4 8 )cycloalkyl(C 2 1 0 )alkanoylamino), (C 4 9 )cycloalkylcarbonyl, hetero(C 4 8 )cycloalkylcarbonyl (optionally substituted with a radical selected from hydroxy, (Cl 1 5 )alkyl, (C 1 5 )alkanoyl, (C 1 5 )alkyloxycarbonyl, (C 6 1 )aryl(C 1 5 )alkyloxycarbonyl and 30 hetero(C 4 8 )cycloalkylcarbonyl), (C 6 10 )aryl(CI-. 5 )alkyloxycarbonyl, carbamoyl, R7 (C 1 5 )alkylcarbamnoyl, di(C I 5 )alkylcarbamoyl, (C 6 4. 1 )arylcarbamoyl, P:\OPER\DCD\53674-96.215 3/8/99 65 (C 610 )aryl(C 1 5 )alkylcarbamoyl, (C 6 -I)aryl(C 1 5 )alkanoyl, (C 7 -I 1 )aroyl, (C 1 5 )alkylsulfonyl, di(C 1 5 )alkylaminosulfoflyl, (C 6 1 )arylsulfonyl or hetero(C 5 8 )arylsulfonyl; R 8 and k 7 are independently (C 3 7 )CYCloalkyl, (C 3 7 )cycloalkyl(C 1 5 )alkyl, pyridyl, thienyl, fliryl, imidazolyl., indolyl, pyridyl(C 1 6 )alkyl, thienyl(C 1 6 )alkyl, ftiryl(C 1 6 )alkyl, imidazolyl(C 1 6 )alkyl, indolyl(C I 6 )alkyl, a group selected from (C 1 5 )alkyl, (C 2 6 )alkyloxy and (C I 5 )alkanoyloxy (which group is optionally substituted with a radical selected from mercapto, carboxy, amino, methylthio, methylsulfonyl, carbamoyl, dimethylcarbamoyl, guanidino and hydroxy, or a protected derivative thereof), a group selected from phenyl, naphthyl, phenyl(C 1 6 )alkyl, naphthyl(C I -)alkyl, (which group is optionally substituted at its aryl ring with one to three radicals selected from amino, hydroxy, chloro, bromo, fluoro, methyl, trifluoromethyl, methoxy and phenyl, or a protected derivative thereof) or together with an adjacent R3 or R 5 forms a divalent radical selected from (C 3 -4methylene and 1 ,2-phenylenedimethylene (which radical is optionally substituted with hydroxy, or a protected derivative thereof, or oxo); each R 1 0 is independently (C 1 5 )alkyl (optionally substituted with one or two radicals selected from amino, cliloro, bromno, fluoro, hydroxy and methoxy or a protected derivative thereof), (C 3 7 )cycloalkyl, (C 3 7 )cycloalkyl(C 1 5 )alkyl, or a group selected from phenyl or phenyl(C 1 6 )alkyl (which group is optionally substituted at its S phenyl ring with one to two radicals selected from amino, chloro, bromo, fluoro, hydroxy, methoxy and optionally halo-substituted methyl, or a protected derivative thereof); R 1 1 is independently (C 1 5 )alkyl, (C 3 7 )CYCloalkyl, (C 3 7 )cycloalkyl(C 1 5 )alkyl or a group selected a. from phenyl, and phenyl(C I 6 )alkyl (which group is optionally substituted at its aryl. ring with one to two radicals selected from amino, chioro, bromno, fluoro, hydroxy, methyl, trifluoromethyl and methoxy); and R' and R 1 are independently (C I 5 )alkyl, (C 3 7 )cycloalkyl, (C 3 7 )cycloalkyl (C 1 5 )alkyl or a group selected from phenyl and phenyl(C 1 6 )alkyl (which group is optionally substituted at its phenyl ring with one to two radicals selected from amino, chloro, bromo, fluoro, hydroxy, methoxy and optionally *~..halo-substituted methyl). The cysteine protease inhibitor of Claim 14 in which each n is 0 to 2; Z is -(CH 2 2 or ~3 -C(R 6 )(R 7 (with the proviso that when n is 0, Z is not -(CH 2 2 each R 1 is hydrogen, 4 8 )alkoxycarbonyl, (C 2 6 )alkanoyl (optionally substituted with a radical selected from P:\OPER\DCD\53674-96.215 318199 66 carboxy, (C 1 5 )alkyloxycarbonyl and hetero(C 4 8 )cycloalkyl(C 4 6 )alkaloylaflilo), -C(O)NR 2 wherein R 21 and R 22 together form aza(C 2 6 )methylene, oxa(C 2 6 )methylene or (C 3 7 )methylene, (C 4 8 )cycloalkylcarboflyl, benzyloxycarbonyl, acetyl, benzoyl or dimethylaminosulfonyl; R8~ and R 7 are independently (C 5 6 )cycloalkyl, (C 5 6 )cycloalkylmethyl, 3-pyridyl, 2-thienyl, 2-furyl, 4-imidazolyl, 3-indolyl, 3-pyridylmethyl, 2-thienylmethyl, 2-fuylmethyl, 4-imidazolylmethyl, 3-indolylmethyl, a group selected from (C 1 5 )alkyl (which group is optionally substituted with a radical selected from mercapto, carboxy, amino, methylthio, methylsulfonyl, carbamoyl, dimethylcarbamoyl, guanidino and hydroxy, or a protected derivative thereof), a group selected from phenyl, 1 -naphthyl, 2-naplithyl, benzyl, 1 -naphthylmethyl, 2-naphthylmethyl and 2-phenylethyl (which group is optionally substituted at its aryl ring with one radical selected from hydroxy, amino, chloro, bromo and fluoro, or, a protected form thereof) or together with an adjacent W? or Wi forms a divalent radical selected from (C 3 4 )methylene and 1 ,2-phenylenedimethylene (which radical is optionally substituted with hydroxy, or a protected derivative thereof, or oxo); each R' 0 is ethyl, (C 5 6 )cycloalkyl, (C 5 6 )cycloalkylmethyl or a group selected from phenyl and benzyl (which group is optionally substituted at its phenyl ring with one radical selected from amino hydroxy, cliloro, bromo or fluoro, or a protected derivative thereof); R 1 '1 is ethyl, cyclo(C 5 6 )alkyl, cyclo(C 5 6 )alkylmethyl or a group selected from phenyl and benzyl (which group is optionally substituted at its phenyl ring with one radical selected from amino hydroxy, chloro, bromo or fluoro, or a protected derivative thereof); and R 1 and R 1 are independently ethyl, (C 5 6 )cycloalkyl, (C 5 6 )cycloalkylmethyl or a group selected from phenyl and benzyl (which group is optionally substituted at its phenyl ring with one radical selected from amino hydroxy, chloro, bromo or fluoro, or a protected derivative thereof).

16. The cysteine protease inhibitor of Claim 15 in which each n is 0 to 1; Z is -C(R 6 )(R 7 each R 1 is hydrogen, tert-butoxycarbonyl, benzyloxycarbonyl, acetyl, 3-carboxypropionyl, 3-methoxycarbonylpropionyl, biotinylaminohexanoyl, phenylacetyl, benzoyl, dimethylaminosulfonyl, benzylsulfonyl, 1 -piperizinylcarbonyl, 4-methy- 1 -lpiperazinylcarbonyl or 4-morpholinylcarbonyl; R8 is butyl, 2-phenylethyl, (Zpmtyluloylthl 2-tert-butoxycarbonylethyl, 2-tert-butoxycarbonylmethyl, I P:\OPER\DCD\53674-96.215 3/8/99 67 4-tert-butoxycarbonylaiobutyl, 4-benzoylaminobutyl or benzyloxymethyl; and R 7 is 3-pyridylmethyl, 2-thienylmethyl, 2-furylmethyl, 4-imidazolylmethyl, 3-indolylmethyl, a group selected from (C I 5 )alkyl (which group is optionally substituted with a radical selected from mercapto, carboxy, amino, methylthio, methylsulfonyl, carbamoyl, dimethylcarbamoyl, guanidino and hydroxy, or a protected derivative thereof), a group selected from benzyl, 1 -naphthylmethyl, 2-naphthylmethyl and 2-phenylethyl (which group is optionally substituted at its aryl ring with one radical selected from hydroxy, amino, chloro, bromo and fluoro, or a protected form thereof) or together with an adjacent R 3 or R 5 forms a divalent radical selected from (C 3 4 )methylene and 1 ,2-phenylenedimethylene (which radical is optionally substituted with hydroxy, or a protected derivative thereof, or oxo).

17. The cysteine protease inhibitor of Claim 16 in which each n is 0; each R 3 R 5 and 1(6 are hydrogen; each R(1 is hydrogen, tert-butxoycarbonyl, benzyloxycarbonyl, biotinylaminohexanoyl, benzoyl, 1 -piperizinylcarbonyl, 4-methyl- I -piperazinylcarbonyl or 4-morpholinylcarbonyl; R8 is butyl, 2-phenylethyl or 2-methylsulfonylethyl; and R 7 is (C 5 )alkyl, 2-methylsulfonylethyl, optionally substituted benzyl, 1 -naphthylmethyl, 2-naphthylmethyl, 3-pyridinylmethyl or 2-methylsulfonylethyl. :18. The cysteine protease inhibitor of Claim 17 in which each R' is *20 1 -piperizinylcarbonyl, 4-methyl- I -piperazinylcarbonyl or 4-morpholinylcarbonyl; R(8 is 2-phenylethyl; and R 7 is optionally substituted benzyl, 1-naphthylmethyl or 2-naphthylmethyl.

19. The cysteine protease inhibitor of Claim 18 in which 1 is 4-morpholinylcarbonyl, 25 1( is 2-phenylethyl, 1(7 is 2-naphthylmethyl and R(9 is ethoxycarbonyl namely ethyl The cysteine protease inhibitor of Claim 18 in which R(1 is 4-morpholinylcarbonyl, R(8 is 2-phenylethyl, 1(7 is benzyl and R?9 is ethoxycarbonyl namely ethyl 30 4S[-4mrhlnlabnl--hnllnlmn]6peyhxnae P:\OPER\DCD\53674-96.215 3/8/99 68

21. The cysteine protease inhibitor of Claim 18 in which R 1 is 4-morpholinylcarbonyl, R 8 is 2-phenylethyl, R 7 is benzyl and R 9 is phenylcarbamoyl namely N2-(4-morpholinylcarbonyl)-Nl -[3-phenyl- 1S-(2-phenylcarbamoylethyl)propyl]- L-phenylalaninamide.

22. The cysteine protease inhibitor of Claim 18 in which R' is 4-morpholinylcarbonyl, R 8 is 2-phenylethyl, R 7 is benzyl and R? is benzylcarbamoyl namely N24(orhlnlcr1 l-'[-pey-S-(2-benzylcarbamoylethyl)propyl]- L-phenylalaninamide.

23. A compound of Formula III: YZ, A R 1 R AnZ 16 I in which: n is 0to 13; A-B represents a linkage selected from -C(O)NR 3 -CH 2 NR 3 -C(O)C11 2 and -NIOC(O)-, wherein R 3 is hydrogen or as defined below; Y is -CH(R 5 or -NR 5 wherein R5~ is hydrogen of s defined below; Z is -(CH 2 2 -C(R 6 )(R 7 or -N(R 7 wherein 1(6 is hydrogen or methyl and R(7 is as defined below; Z' is -(CH 2 2 -C(R 6 )(R 8 or -N(R 8 wherein R 6 is hydrogen or methyl. and R(8 is as defined below; R' is hydrogen, alkyloxycarbonylalkanoyl, alkyloxycarbonyl, alkanoyl. (optionally substituted with a radical selected from carboxy, alkyloxycarbonyl. and heterocycloalkylalkanoylamino), cycloalkylcarbonyl, heterocycloalkylcarbonyl (optionally substituted with a radical selected from hydroxy, alkyl, alkanoyl, alkyloxycarbonyl, arylalkyloxycarbonyl and heterocycloalkylcarbonyl), arylalkyloxycarbonyl, carbamoyl, alkylcarbamoyl, dialkylcarbamoyl, arylcarbamoyl, arylalkylcarbamoyl, arylalkanoyl, aroyl, -'\alkylsulfonyl, dialkylaminosulfonyl, arylsulfonyl or heteroarylsulfonyl; P:\OPER\DCD\53674-96.273 30/9/99 -69- R 7 and R 8 are independently (C 1 -5)alkyl (optionally substituted with a radical selected from hydroxy, amino, alkylamino, dialkylamino, uriedo, mercapto, alkylthio, carboxy, carbamoyl, alkylcarbamoyl, dialkylcarbamoyl, alkylsulfonyl and guanidino, or a protected derivative thereof), (C 3 .)cycloalkyl, (C 3 7 )cycloalkyl(C- 5 )alkyl, pyridyl, thienyl, furyl, imidazolyl, indolyl, pyridyl(Cl- 6 )alkyl, thienyl(C. 6 )alkyl, fuiryl(C.)alkyl, imidazolyl(C 1 6 )alkyl, indolyl(Cl.- 6 )alkyl, a group selected from (C 1 -5)alkyl, (C 2 6 )alkyloxy and (Cl-5)alkanoyloxy (which group is optionally substituted with a radical selected from mercapto, carboxy, amino, methylthio, methylsulfonyl, carbamoyl, dimethylcarbamoyl, guanidino and hydroxy, or a protected derivative thereof), a group selected from phenyl, 10 naphthyl, phenyl(Cl- 6 )alkyl, naphthyl(C 1 6 )alkyl, (which group is optionally substituted at its aryl ring with one to three radicals selected from hydroxy, amino, chloro, bromo, iodo, fluoro, methyl, trifluoromethyl, methoxy and phenyl, or a protected derivative thereof) or together with an adjacent R 3 or R 5 forms a divalent radical selected from (C 3 4 )methylene and 1,2-phenylenedimethylene (which radical is optionally substituted with hydroxy, or a protected derivative thereof, or oxo); R 15 is hydrogen, methyl, fluoro or a group selected from Formulae and S S.. S S. SO S 0 0 S. *505 0 0@ 0 *050 S 0 0 zA B z (ORao (a) ZB"' ~A)Y R1 0 (b) .0. 009 wherein each n, A, B, Y, Z and R' are as defined above and Ro 10 is hydrogen, alkyl (optionally substituted with one or more radicals selected from amino, halo, hydroxy, alkyloxy, nitro, alkylsulfonyl and arylsulfonyl, or a protected derivative thereof), cycloalkyl, cycloalkylalkyl or a group selected from aryl and arylalkyl (which group is optionally substituted at its aryl ring with one to two radicals selected from amino, halo, hydroxy, optionally halo-substituted alkyl, alkyloxy, nitro, alkylsulfonyl and arylsulfonyl, or a protected derivative thereof); and R 1 6 is a group selected from phenyl or (C 5 6 )heteroaryl (which group is optionally substituted with at least one radical selected from alkylcarbamoyl, dialkylcarbamoyl, alkyloxycarbonyl, alkylsulfinamoyl, dialkylsulfinamoyl, alkylsulfonyl, carboxy, nitro, P:\OPERkDCD\53674-96.273 30/9/99 -69A- sulfinamoyl, sulfo, carbamoyl, phosphono, alkyloxyphosphinyl, dialkyloxyphosphinyl, alkanoyl, cyano, alkylsulfinyl, sulfamoyl, alkylsulfamoyl, dialkylsulfamoyl, alkyloxysulfonyl, alkylsulfonimidoyl, aryl, heteroaryl, hydroxy, alkyloxy, optionally S. 0O 0*S 0 S. 0 0 0S 0eS@ SS 55 S0 0 0 *0 S 0 @00 5 0e SS 6 *00* 0S 0 0 0 *00* 005505 6 0 0O 5 0 005 0 P\kOPER\DCD\53674-96.215 3/8/99 70 halo-substituted alkyl, arylalkyl, halo, 17 3 wherein each R 1 7 is independently alkyl, aryl or arylalkyl, or -N(R 18 2 wherein each R 1 8 is independently hydrogen, alkyl, aryl or arylalkyl); and the pharmaceutically acceptable salts; individual isomers and mixtures of isomers thereof.

24. The cysteine protease inhibitor of Claim 23 in which each n is 0 to 5; each A-B represents a linkage selected from -C(O)NR 3 each Y is -NR 5 each Z is -(CH 2 2 or -C(R 6 )(R 7 Z' is -CH(R 8 each R' is hydrogen, alkyloxycarbonylalkanoyl. of overall 3 to carbon atoms, (C I 9 )alkoxycarbonyl, (C 2 1 )alkanoyl (optionally substituted with a radical selected from carboxy, (C 1 9 )Ikyoyarbonyi and hetero(C 4 8 )cycloalkyl(C 2 10 )alkanoylamino), (C 4 9 )cycloalkylcarbonyl, hetero(C 4 8 )cycloalkylcarbonyl (optionally substituted with a radical selected from hydroxy, (C 1 5 )alkyl, (C 1 5 )alkanoyl, (C 1 5 )alkyloxycarbonyl, (C 6 10 )aryl(C 1 5 )alkyloxycarbonyl and hetero(C 4 8 )cycloalkylcarbonyl), (C 6 I )aryl(C 1 5 )alkyloxycarbonyl, carbamoyl, (C 1 5 )alkylcarbamoyl, di(C 1 5 )alkylcarbamoyl, (C 6 1 )arylcarbamoyl, (C 6 1 )arYl(C 1 5 )alkylcarbamoyl, (C 6 I )aryl(C I 5 )alkanoyl, (C 7 1 1 )aroyl, (C 1 5 )aklsulfonyl, di(C 1 5 )alkylamninosulfonyl, (C 6 I )arylsulfonyl or hetero(C 5 8 )arylsulfonyl; R 8 and R 7 are independently (C 3 7 )cycloalkyl, (C 3 7 )cycloalkyl(C I 5 )alkyl, pyridyl, thienyl, furyl, 4 4, imidazolyl, indolyl, pyridyl(C 1 6 )alkyl, thienyl(C 1 -)alkyl, fiiryl(C 16 )alkyl, imidazolyl(C 1 6 )alkyl, indolyl(C 1 6 )alkyl, a group selected from (C 1 5 )alkyl, (C 2 6 )alkyloxy and (C 1 5 )alkanoyloxy (which group is optionally substituted with a radical selected from mercapto, carboxy, amino, methylthio, methylsulfonyl, carbamoyl, dimethylcarbamnoyl, tee 9guanidino and hydroxy, or a protected derivative thereof), a group selected from phenyl, e naphthyl, phenyl(C 1 6 )alkyl, naphthyl(C 1 6 )alkyl, (which group is optionally substituted at its aryl ring with one to three radicals selected from amino, hydroxy, chioro, bromo, fluoro, methyl, trifluoromethyl, methoxy and phenyl, or a protected derivative thereof) or together with an adjacent R 3 or R 5 forms a divalent radical selected from (C 3 .4methylene and 1 ,2-phenylenedimethylene (which radical is optionally substituted with hydroxy, or a protected derivative thereof, or oxo); R 10 is (C 1 5 )alkyl (optionally substituted with one or two radicals selected from amino, chioro, bromo, fluoro, hydroxy and methoxy or a Sprotected derivative thereof), (C 3 7 )cycloalkyl, (C 37 )cycloalkyl(C I 5 )alkyl, or a group P:\OPER\DCO\53674-96.215 3/8199 71 selected from phenyl or phenyl(C 1 6 )alkyl (which group is optionally substituted at its phenyl ring with one to two radicals selected from amino, chloro, bromo, fluoro, hydroxy, methoxy and optionally halo-substituted methyl, or a protected derivative thereof); and R 1 6 is a group selected from 2-furyl, 2-thienyl, 2-pyrrolyl, 2-phosholyl, 2-arsolyl, 3-pyridyl or 3-phosphorinyl (which group is optionally substituted with at least one radical selected from (C 1 5 )alkylcarbamoyl, di(C 1 5 )alkylcarbamoyl, (C 1 5)alkylsulfinamoyl, di(C 1 5 )alkylsulfinamoyl, (C 1 5 )alkylsulfonyl, carboxy, nitro, sulfinamoyl, sulfo, carbamoyl, phosphono, (C I 5 )alkyloxyphosphinyl, di(C 1 5 )alkyloXyphosphinyl, (C 1 5 )alkanoyl, cyano, (C 1 5 )alkylsulfinyl, sulfamoyl, (C 1 5 )alkylsulfamoyl, di(C 1 5 )alkyisulfamoyi, (C 1 5 )aikyioxysuifonyi, (C 1 5 )alkylsulfonimidoyl, phenyl, naphthyl, pyridyl, thienyl, fuiryl, imidazolyl, indolyl, hydroXY, (C 1 5 )alkyloxy, optionally halo-substituted (C 1 5 )alkyl, benzyl, halo, 17 3 wherein each R 17 is independently (C 1 5 )alkyl, phenyl or benzyl, or -N(R 8 2 wherein each R 18 is independently hydrogen, (C 1 5 )alkyl, phenyl or benzyl). The cysteine protease inhibitor of Claim 24 in which each n is 0 to 2; Z is -(CH 2 2 or -C(R 6 7 (with the proviso that when n is 0, Z is not -(CH 2 2 each R1 is hydrogen, too(C 4 8 )alkoxycarbonyl, (C 2 6 )alkanoyl (optionally substituted with a radical selected from carboxy, (C 1 5 )alkyloxycarbonyl and hetero(C 4 8 )cycloalkyl(C 4 6 )alkanoylamino), 5: 20 -C(O)NR 21 R 22 wherein R 21 and R 2 together form aza(C 2 6 )methylene, oxa(C 2 6 )methylene *too or (C 3 7 )methylene, (C 4 8 )cycloalkylcarbonyl, benzyloxycarbonyl, acetyl, benzoyl or dimethylaminosulfonyl; R 8 and R 7 are independently (C 5 6 )cycloalkyl, o..G 0(C 5 6 )cycloalkylmethyl, 3-pyridyl, 2-thienyl, 2-furyl, 4-imidazolyl, 3-indolyl, to. 2 0-pyridylmethyl, 2-thienylmethyl, 2-fuirylmethyl, 4-imidazolylmethyl, 3-indolylmethyl, acetoxy, (C 1 5 )alkyl (optionally substituted with a radical selected from mercapto, carboxy, amino, methylthio, methylsulfonyl, carbamoyl, dimethylcarbamoyl, guanidino and hydroxy, or a protected derivative thereof) a group selected from phenyl, I1-naphthyl., 2-naphthyl, benzyl, 1-naphthylmethyl, 2-naphthylmethyl and 2-phenylethyl (which group is optionally substituted at its aryl ring with one radical selected from hydroxy, amino, chloro, bromo and fluoro, or a protected form thereof) or together with an adjacent W 3 or R 5 forms a \\divalent radical selected from (C 3 4 )methylene and 1 ,2-phenylenedimethylene (which radical P:\OPER\DCD\53674-96.215 3/8/99 72 is optionally substituted with hydroxy, or a protected derivative thereof, or oxo); each RI 0 is ethyl, (Cs 5 6 )cycloalkyl, (C 5 6 )cycloalkylmethyl or a group selected from phenyl and benzyl (which group is optionally substituted at its phenyl ring with one radical selected from amino hydroxy, chloro, bromo or fluoro, or a protected derivative thereof); and R' 16 is a group selected from 2-furyl, 2-thienyl, 2-pyrrolyl, 2-phosholyl, 2-arsolyl, 2-pyridyl or 3-phosphorinyl (which group is optionally substituted with at least one radical selected from methylcarbamoyl, dimethylcarbamoyl, methyloxycarbonyl, methylsulfinamoyl, dimethylsulfinamoyl, methylsulfonyl, carboxy, nitro, sulfinamoyl, sulfo, carbamoyl, phosphono, methyloxyphosphinyl, dimethyloxyphosphinyl, formyl, cyano, methylsulfinyl, iV sulfamoyl, methyisulfamoy, dimethyisulamoyi, methoxysulfony, methylsulfonimidoyl, phenyl, naphthyl, pyridyl, thienyl, furyl, imidazolyl, indolyl, hydroxy, methoxy, methyl, trifluromethyl, benzyl, halo, -+N(R 1 7 3 wherein each R 1 7 is independently methyl, phenyl or benzyl, or -N(R' 8 2 wherein each R' 18 is independently hydrogen, methyl, phenyl or benzyl).

26. The cysteine protease inhibitor of Claim 25 in which each n is 0 to 1; Z is -C(R 6 )(R 7 each R 1 is hydrogen, tert-butoxycarbonyl, benzyloxycarbonyl, acetyl, 3-carboxypropionyl, 3-methoxycarbonylpropionyl, biotinylaminohexanoyl, phenylacetyl, benzoyl, dimethylaminosulfonyl, benzylsulfonyl, 1 -piperizinylcarbonyl, 4-methyl- 1-piperazinylcarbonyl or 4-morpholinylcarbonyl; R 8 is butyl, 2-phenylethyl, 2-methylsulfonylethyl, 2-tert-butoxycarbonylethyl, 2-tert-b .toxycarbonylmethyl, 4-tert-butoxycarbonylaminobutyl, 4-benzoylaminobutyl or benzyloxymethyl; and R 7 is S. 3-pyridylmethyl, 2-thienylmethyl, 2-furylmethyl, 4-imidazolylmethyl, 3-indolylmethyl, (C 1 -5)alkyl (optionally substituted with a radical selected from mercapto, carboxy, amino, S methylthio, methylsulfonyl, carbamoyl, dimethylcarbamoyl, guanidino and hydroxy, or a protected derivative thereof), a group selected from benzyl, 1 -naphthylmethyl, I 2-naphthylmethyl and 2-phenylethyl (which group is optionally substituted at its aryl ring with one radical selected from hydroxy, amino, chloro, bromo and fluoro, or a protected form thereof) or together with an adjacent R 3 or R 5 forms a divalent radical selected from (C 3 4 )methylene and 1,2-phenylenedimethylene (which radical is optionally substituted with AQ hydroxy, or a protected derivative thereof, or oxo). P:\OPER\DCD\53674-96.215 3/8/99 73

27. The cysteine protease inhibitor of Claim 26 in which each n is 0; each R 3 R 5 and R 6 are hydrogen; each R' is hydrogen, tert-butxoycarbonyl, benzyloxycarbonyl, biotinylaminohexanoyl, benzoyl, 1 -piperizinylcarbonyl, 4-methyl-i -piperazinylcarbonyl or 4-morpholinylcarbonyl; R 8 is butyl, 2-phenylethyl or 2-methylsulfonylethyl; and R 7 is (C 1 5 )alkyl, 2-methylsulfonylethyl, optionally substituted benzyl, 1 -naphthylmethyl, 2-naphthylmethyl, 3-pyridinylmethyl or 2-methylsulfonylethyl.

28. The cysteine protease inhibitor of Claim 27 in which each R 1 is 1 -piperizinylcarbonyl, 4-methyl-i -piperazinylcarbonyl or 4 -morpholinylcarbonyl; R 8 is 2-phenylethyl; and R is optionally subsIULtd benyl, 1-inaphthyimethyl or 2-naphthylmethyl.

29. The cysteine protease inhibitor of Claim 28 in which R' is 4 -morpholinylcarbonyl, R 8 is 2-phenylethyl, R 7 is benzyl, R' 5 is hydrogen and R 16 is 4-methoxyphenyl, namely N 2 -4-morpholinylcarbonyl-N'- {3-phenyl-iS-[ 2 4 -methoxyphenyl)ethyl]propyl}- L-phenylalaninamide. The cysteine protease inhibitor of Claim 28 in which R 1 is 4 -morpholinylcarbonyl, R 8 is 2-phenylethyl, R 7 is benzyl, R'15 is hydrogen and R' 6 is 4-aminophenyl, namely N 2 -(4-morpholinylcarbonyl)-N'- {3-phenyl- IS- [2-(4-aminophenyi)ethyl]propyl} L-phenylalaninamide. S:

31. A cysteine protease inhibitor for inhibiting a cysteine protease comprising reversibly binding a cysteine protease inhibitor to a cysteine protease, wherein said inhibitor comprises *S 25 the cysteine protease inhibitor of Claim 1, 13, or 23.

32. A method for treating a condition capable of amelioration by inhibition of a cysteine protease in an animal in need thereof, which method comprises administering to such animal a therapeutically effective amount of the cysteine protease inhibitor of Claim 1, 13, or 23. 3. A pharmaceutical composition comprising a therapeutically effective amount of the P:\OPER\DCD\53674-96.215 3/8/99 -74- cysteine protease inhibitor of Claim 1, 13, or 23 or an individual isomer thereof, a mixture of isomers thereof, or the pharmaceutically acceptable salt or salts thereof, in combination with one or more pharmaceutically acceptable excipients.

34. A process for the preparation of a compound of Formula IV: O Re z _A N in which: nis 0 to 12; A-B represents a linkage selected from -C(O)NR 3 -CH 2 NR-, -C(O)CH 2 and -NR 3 wherein R 3 is hydrogen or as defined below; Y is -CH(R 5 or -N(R 5 wherein R 5 is hydrogen or as defined below; Z is -(CH2) 2 -C(R 6 )(R 7 or -N(R 7 wherein R6 is hydrogen or methyl and R 7 is as defined below; Z 1 is -(CH2) 2 or -N(R 8 wherein R6 is hydrogen or methyl and R 8 is as defined below; R6 is hydrogen or methyl and R is as defined below; **a R' is hydrogen, alkyloxycarbonylalkanoyl, alkyloxycarbonyl, alkanoyl (optionally substituted with a radical selected from carboxy, alkyloxycarbonyl and heterocycloalkylalkanoylamino), cycloalkylcarbonyl, heterocycloalkylcarbonyl (optionally 25 substituted with a radical selected from hydroxy, alkyl, alkanoyl, alkyloxycarbonyl, arylalkyloxycarbonyl and heterocycloalkylcarbonyl), arylalkyloxycarbonyl, carbamoyl, alkylcarbamoyl, dialkylcarbamoyl, arylcarbamoyl, arylalkylcarbamoyl, arylalkanoyl, aroyl, alkylsulfonyl, dialkylaminosulfonyl, arylsulfonyl or heteroarylsulfonyl; R 7 and R8 are independently hydrogen, alkyl (optionally substituted with a radical selected from hydroxy, amino, alkylamino, dialkylamino, uriedo, mercapto, alkylthio, i R, carboxy, carbamoyl, alkylcarbamoyl, dialkylcarbamoyl, alkylsulfonyl and guanidino, or a I P:\OPER\DCD\53674-96.215 3/8/99 protected derivative thereof), cycloalkyl, cycloalkylalkyl, heteroaryl, heteroarylalkyl, a group selected from aryl and arylalkyl (which group is optionally substituted at its aryl ring with one to three radicals selected from hydroxy, amino, guanidino, halo, optionally halo-substituted alkyl, alkyloxy and aryl, or a protected derivative thereof) or together with an adjacent R 3 or R 5 forms a divalent radical selected from a divalent radical selected from (C 3 4 )methylene and 1,2-phenylenedimethylene (which radical is optionally substituted with hydroxy, or a protected derivative thereof, or oxo); and R 2 0 is cyano, -S(0) 2 R 2 -CH 2 S(0) 2 R 2 -CH 2 CH(R 4 )S(O) 2 R 2 -(CH 2 2 C(O)OR, -(CH 2 2 P(O)(OR' 0 -(CH2)2S(O)(NR')R'o, -(CH2)2C(O)R", -(CH 2 2 S(O)R", V 2?NRI2 13 rU c nS\ WTDr2D 13 N 1 JrtrIl4 /2 I N 14 or \v v.2 112/2 2 12* r 2 riX r1 2 2 i,U) 2 1NK 1 or -CH 2 CHRsR 1 6 wherein R 2 is hydrogen, alkyl (optionally substituted with one or more radicals selected from amino, halo, hydroxy, alkyloxy, nitro, alkylsulfonyl and arylsulfonyl, or a protected derivative thereof), cycloalkyl, cycloalkylalkyl or a group selected from aryl and arylalkyl (which group is optionally substituted at its aryl ring with one to two radicals selected from amino, halo, hydroxy, optionally halo-substituted alkyl, alkyloxy, nitro, alkylsulfonyl and arylsulfonyl, or a protected derivative thereof), R 4 is hydrogen, alkyl or arylalkyl, each R 1 0 is independently hydrogen, alkyl (optionally substituted with one or more radicals selected from amino, halo, hydroxy, alkyloxy, nitro, alkylsulfonyl and arylsulfonyl, j: or a protected derivative thereof), cycloalkyl, cycloalkylalkyl or a group selected from aryl 20 and arylalkyl (which group is optionally substituted at its aryl ring with one to two radicals selected from amino, halo, hydroxy, optionally halo-substituted alkyl, alkyloxy, nitro, alkylsulfonyl and arylsulfonyl, or a protected derivative thereof), R' I is hydrogen, alkyl, perfluoroalkyl, cycloalkyl, cycloalkylalkyl, perfluoroaryl, perfluoroarylakyl or a group selected from aryl and arylalkyl (which group is optionally substituted at its aryl ring with 25 one to two radicals selected from amino, halo, hydroxy, optionally halo-substituted alkyl, alkyloxy, nitro, alkylsulfonyl and arylsulfonyl, or a protected derivative thereof), R 1 2 and R 1 3 are independently hydrogen, alkyl, cycloalkyl, cycloalkylalkyl, aryl or aralkyl, R 14 is -C(O)OR'O, in which R 10 is as defined above, or a group selected from Formula and .1 M I _M P:\OPER\DCD\53674-96.215 3/8/99 -76- 0 BA OR Z Ri o (b) wherein each n, A, B, Y, Z, R' and R 10 are as defined above, R 15 is hydrogen, methyl, fluoro or a group selected from Formulae and as defined above, and R1 6 is a group selected from phenyl or (C5- 6 )heteroaryl (which group is optionally substituted with at least one radical selected from alkylcarbamoyl, dialkylcarbamoyl, alkyloxycarbonyl, alkylsulfinamoyl, dialkyisulfinamoyl, alKylsulfonyl, carboxy, ILtru, sulminu yl, sulifo, carbamlloyl, phosphonlull alkyloxyphosphinyl, dialkyloxyphosphinyl, alkanoyl, cyano, alkylsulfinyl, sulfamoyl, alkylsulfamoyl, dialkylsulfamoyl, alkyloxysulfonyl, alkylsulfonimidoyl, aryl, heteroaryl, hydroxy, alkyloxy, optionally halo-substituted alkyl, arylalkyl, halo, -fN(R 17 3 wherein each R17 is independently alkyl, aryl or arylalkyl, or -N(R' 8 2 wherein each R 18 is independently hydrogen, alkyl, aryl or arylalkyl); and the pharmaceutically acceptable salts, individual isomers and mixtures of isomers thereof; which process comprises: reacting an amine of Formula V: R 2 H 2 N R 2 with a compound of Formula VI: 0 R. YZAB Z OH VI in which each n, A, B, Y, Z, R 1 R and R 2 0 are as defined above; and optionally further converting a non-salt form of a compound of Formula IV into a pharmaceutically acceptable salt; optionally further converting a salt form of a compound of Formula IV into P:\OPER\DCD\53674-96.215 3/8/99 -77- non-salt form; and optionally further separating a compound of Formula IV into individual stereoisomers.

35. A process for the preparation of a compound of Formula IV: 0 R 8 R1 Z B Z A B Z N R2 H in which: n is 0 to 12; A-B represents a linkage selected from -C(O)NR 3 -CH 2 NR-, -C(O)CH 2 and -NR 3 wherein R 3 is hydrogen or as defined below; Y is -CH(RS)- or -N(R 5 wherein R 5 is hydrogen or as defined below; Z is -(CH 2 2 -C(R 6 )(R 7 or -N(R 7 wherein R 6 is hydrogen or methyl and R7 is as defined below; Z' is -(CH 2 2 -C(R 6 or -N(R 8 wherein R 6 is hydrogen or methyl and R 8 is as defined below; R 6 is hydrogen or methyl and R 7 is as defined below; R' is hydrogen, alkyloxycarbonylalkanoyl, alkyloxycarbonyl, alkanoyl (optionally substituted with a radical selected from carboxy, alkyloxycarbonyl and heterocycloalkylalkanoylamino), cycloalkylcarbonyl, heterocycloalkylcarbonyl (optionally substituted with a radical selected from hydroxy, alkyl, alkanoyl, alkyloxycarbonyl, arylalkyloxycarbonyl and heterocycloalkylcarbonyl), arylalkyloxycarbonyl, carbamoyl, alkylcarbamoyl, dialkylcarbamoyl, arylcarbamoyl, arylalkylcarbamoyl, arylalkanoyl, aroyl, alkylsulfonyl, dialkylaminosulfonyl, arylsulfonyl or heteroarylsulfonyl; R7 and R 8 are independently hydrogen, alkyl (optionally substituted with a radical selected from hydroxy, amino, alkylamino, dialkylamino, uriedo, mercapto, alkylthio, carboxy, carbamoyl, alkylcarbamoyl, dialkylcarbamoyl, alkylsulfonyl and guanidino, or a 1 z protected derivative thereof), cycloalkyl, cycloalkylalkyl, heteroaryl, heteroarylalkyl, a group P:\OPER\DCD\53674-96.215 3/8/99 -78- selected from aryl and arylalkyl (which group is optionally substituted at its aryl ring with one to three radicals selected from hydroxy, amino, halo, optionally halo-substituted alkyl, alkyloxy and aryl, or a protected derivative thereof) or together with an adjacent R 3 or R forms a divalent radical selected from a divalent radical selected from (C 3 4 )methylene and 1,2-phenylenedimethylene (which radical is optionally substituted with hydroxy, or a protected derivative thereof, or oxo); and R 20 is -S(0) 2 R 2 wherein R 2 is hydrogen, alkyl (optionally substituted with one or more radicals selected from amino, halo, hydroxy, alkyloxy, nitro, alkylsulfonyl and arylsulfonyl, or a protected derivative thereof), cycloalkyl, cycloalkylalkyl or a group selected from aryl and arylakyi (whiUch1 group is optionally su stituted at its aryl ring wit one to two radicals selected from amino, halo, hydroxy, optionally halo-substituted alkyl, alkyloxy, nitro, alkylsulfonyl and arylsulfonyl, or a protected derivative thereof), and the pharmaceutically acceptable salts, individual isomers and mixtures of isomers thereof; which process comprises: reacting a compound of Formula VII: 0 RI YZA B Z"A Z' NI VII with an aldehyde of the formula R 8 CHO and a sodium sulfinate of the formula R 2 S(O)ONa, in which each n, A, B, Y, Z, R 1 and R 8 are as defined above; optionally further converting a non-salt form of a compound of Formula IV into a pharmaceutically acceptable salt; 25 optionally further converting a salt form of a compund of Formula IV into non-salt form; and optionally further separating a compound of Formula IV into individual Sstereoisomers.

36. A process for the preparation of a compound of Formula IV: P:\OPER\DCD\53674-96.215 3/8/99 -79- 0 R OR 20 R Z BZ N R H in which: n is 0 to 12; A-B represents a linkage selected from -C(O)NR 3 -CH 2 NR 3 -C(O)CH 2 and -NR 3 wherein R 3 is hydrogen or as defined below; 5X XT/-M 5\ I "5 I l Y is -o R or -N(S whereuin I. Is hiyuurogll U ias udeindu UIuw, Z is -(CH 2 2 -C(R)(R 7 or -N(R 7 wherein R 6 is hydrogen or methyl and R 7 is as defined below; Z 1 is -(CH 2 2 -C(R 6 or -N(R 8 wherein R 6 is hydrogen or methyl and R 8 is as defined below; R 6 is hydrogen or methyl and R 7 is as defined below; R' is hydrogen, alkyloxycarbonylalkanoyl, alkyloxycarbonyl, alkanoyl (optionally substituted with a radical selected from carboxy, alkyloxycarbonyl and heterocycloalkylalkanoylamino), cycloalkylcarbonyl, heterocycloalkylcarbonyl (optionally substituted with a radical selected from hydroxy, alkyl, alkanoyl, alkyloxycarbonyl, arylalkyloxycarbonyl and heterocycloalkylcarbonyl), arylalkyloxycarbonyl, carbamoyl, alkylcarbamoyl, dialkylcarbamoyl, arylcarbamoyl, arylalkylcarbamoyl, arylalkanoyl, aroyl, alkylsulfonyl, dialkylaminosulfonyl, arylsulfonyl or heteroarylsulfonyl; R 7 and R 8 are independently hydrogen, alkyl (optionally substituted with a radical selected from hydroxy, amino, alkylamino, dialkylamino, uriedo, mercapto, alkylthio, carboxy, carbamoyl, alkylcarbamoyl, dialkylcarbamoyl, alkylsulfonyl and guanidino, or a :protected derivative thereof), cycloalkyl, cycloalkylalkyl, heteroaryl, heteroarylalkyl, a group selected from aryl and arylalkyl (which group is optionally substituted at its aryl ring with one to three radicals selected from hydroxy, amino, halo, optionally halo-substituted alkyl, alkyloxy and aryl, or a protected derivative thereof) or together with an adjacent R3 or forms a divalent radical selected from a divalent radical selected from (C 3 4 )methylene and /\CJ R1,2-phenylenedimethylene (which radical is optionally substituted with hydroxy, or a P:\OPER\DCD\53674-96.215 5/8/99 protected derivative thereof, or oxo); and R 20 is -S(0) 2 R 2 wherein R 2 is hydrogen, alkyl (optionally substituted with one or more radicals selected from amino, halo, hydroxy, alkyloxy, nitro, alkylsulfonyl and arylsulfonyl, or a protected derivative thereof), cycloalkyl, cycloalkylalkyl or a group selected from aryl and arylalkyl (which group is optionally substituted at its aryl ring with one to two radicals selected from amino, halo, hydroxy, optionally halo-substituted alkyl, alkyloxy, nitro, alkylsulfonyl and arylsulfonyl, or a protected derivative thereof); and the pharmaceutically acceptable salts, individual isomers and mixtures of isomers thereof; which process comprises: reacting a compound of the formula NH 2 P, wherein P is a protective group, with an aldehyde of the formula R 8 CHO and a sodium sulfinate of the formula R 2 S(O)ONa and then deprotecting to give a compound of Formula VIII: R H 2 N S(O) 2 R 2 20 in which R 2 and R 8 are as defined above; and reacting the compound of Formula VIII with a compound of Formula VI: R Z BY Z OH a. VI in which each n, A, B, Y, Z, and R 1 are as defined above; optionally further converting a non-salt form of a compound of Formula IV into a pharmaceutically acceptable salt; optionally further converting a salt form of a compund of Formula IV into I M P:\OPER\DCD\53674-96.215 3/8/99 -81- non-salt form; and optionally further separating a compound of Formula IV into individual stereoisomers.

37. A process for the preparation of a compound of Formula IV: 0 R R Z A B ZA BZ N n H in which: n is 0 to 12; A-B represents a linkage selected from -C(O)NR 3 -CH 2 NR 3 -C(O)CH 2 and -NR 3 wherein R 3 is hydrogen or as defined below; Y is -CH(R 5 or -N(R 5 wherein R 5 is hydrogen or as defined below; Z is -(CH 2 2 -C(R 6 )(R 7 or -N(R 7 wherein R 6 is hydrogen or methyl and R 7 is as defined below; Z 1 is -(CH2 2 -C(R 6 )(R 8 or wherein R 6 is hydrogen or methyl and R 8 is as defined below; 20 R 6 is hydrogen or methyl and R 7 is as defined below; R 1 is hydrogen, alkyloxycarbonylalkanoyl, alkyloxycarbonyl, alkanoyl (optionally S. substituted with a radical selected from carboxy, alkyloxycarbonyl and heterocycloalkylalkanoylamino), cycloalkylcarbonyl, heterocycloalkylcarbonyl (optionally substituted with a radical selected from hydroxy, alkyl, alkanoyl, alkyloxycarbonyl, 25 arylalkyloxycarbonyl and heterocycloalkylcarbonyl), arylalkyloxycarbonyl, carbamoyl, alkylcarbamoyl, dialkylcarbamoyl, arylcarbamoyl, arylalkylcarbamoyl, arylalkanoyl, aroyl, alkylsulfonyl, dialkylaminosulfonyl, arylsulfonyl or heteroarylsulfonyl; R 7 and R 8 are independently hydrogen, alkyl (optionally substituted with a radical selected from hydroxy, amino, alkylamino, dialkylamino, uriedo, mercapto, alkylthio, carboxy, carbamoyl, alkylcarbamoyl, dialkylcarbamoyl, alkylsulfonyl and guanidino, or a 3 protected derivative thereof), cycloalkyl, cycloalkylalkyl, heteroaryl, heteroarylalkyl, a group P:\OPER\DCD\53674-96.215 5/8/99 -82- selected from aryl and arylalkyl (which group is optionally substituted at its aryl ring with one to three radicals selected from hydroxy, amino, halo, optionally halo-substituted alkyl, alkyloxy and aryl, or a protected derivative thereof) or together with an adjacent R 3 or R forms a divalent radical selected from a divalent radical selected from (C 3 4 )methylene and 1,2-phenylenedimethylene (which radical is optionally substituted with hydroxy, or a protected derivative thereof, or oxo); and R 20 is -CH 2 S(0) 2 R 2 wherein R 2 is hydrogen, alkyl (optionally substituted with one or more radicals selected from amino, halo, hydroxy, alkyloxy, nitro, alkylsulfonyl and arylsulfonyl, or a protected derivative thereof), cycloalkyl, cycloalkylalkyl or a group selected from aryl and arylalkyl (which group is optionally substituted at its aryl ring with one to two radicals selected from amino, halo, hydroxy, optionally halo-substituted alkyl, alkyloxy, nitro, alkylsulfonyl and arylsulfonyl, or a protected derivative thereof); and the pharmaceutically acceptable salts, individual isomers and mixtures of isomers thereof; which process comprises: reacting a compound of Formula IX: R 8 PHN L *o 0 with a thiolate anion of the formula R 2 in which L is a leaving group and R 2 and R 8 are as defined above, to give a compound of Formula X: S 25 o SR 2 25 °PHN oxidizing the compound of Formula X to give a compound of Formula XI: R 8 0 P. S(O) 2 R 2 PHN P:\OPER\DCD\53674-96.215 3/8/99 -83- and reacting the compound of Formula XI with a compound of Formula VI: 0 R5 ZA B, Z "A Z OH R Zn VI in which each n, A, B, Y, Z and R 1 are as defined above; optionally further converting a non-salt form of a compound of Formula IV into a pharmaceutically acceptable salt; optionally further converting a salt form of a compund of Formula IV into non-salt form; and optionally further separating a compound of Formula IV into individual stereoisomers.

38. A process for the preparation of a compound of Formula IV: O R 8 in which: n is 0 to 12; 25 A-B represents a linkage selected from -C(O)NR 3 -CH 2 NR 3 -C(O)CH 2 and -NR 3 wherein R 3 is hydrogen or as defined below; 4o Y is -CH(RS) or -N(RS) wherein R 5 is hydrogen or as defined below; Z is -(CH2)2- -C(R6)(R) or -N(R7) wherein R 6 is hydrogen or methyl and R 7 is as defined below; Z 1 is -(CH 2 2 -C(R 6 or -N(R 8 wherein R 6 is hydrogen or methyl and R 8 is as defined below; P:\OPER\DCD\53674-96.215 -3/8/99 -84- R 6 is hydrogen or methyl and R 7 is as defined below; R 1 is hydrogen, alkyloxycarbonylalkanoyl, alkyloxycarbonyl, alkanoyl (optionally substituted with a radical selected from carboxy, alkyloxycarbonyl and heterocycloalkylalkanoylamino), cycloalkylcarbonyl, heterocycloalkylcarbonyl (optionally substituted with a radical selected from hydroxy, alkyl, alkanoyl, alkyloxycarbonyl, arylalkyloxycarbonyl and heterocycloalkylcarbonyl), arylalkyloxycarbonyl, carbamoyl, alkylcarbamoyl, dialkylcarbamoyl, arylcarbamoyl, arylalkylcarbamoyl, arylalkanoyl, aroyl, alkylsulfonyl, dialkylaminosulfonyl, arylsulfonyl or heteroarylsulfonyl; R 7 and R 8 are independently hydrogen, alkyl (optionally substituted with a radical selected from hydroxy, amino, alkylamino, dialkylamino, uriedo, mercapto, alkylthio, carboxy, carbamoyl, alkylcarbamoyl, dialkylcarbamoyl, alkylsulfonyl and guanidino, or a protected derivative thereof), cycloalkyl, cycloalkylalkyl, heteroaryl, heteroarylalkyl, a group selected from aryl and arylalkyl (which group is optionally substituted at its aryl ring with one to three radicals selected from hydroxy, amino, halo, optionally halo-substituted alkyl, alkyloxy and aryl, or a protected derivative thereof) or together with an adjacent R 3 or R forms a divalent radical selected from a divalent radical selected from (C 3 4 )methylene and 1,2-phenylenedimethylene (which radical is optionally substituted with hydroxy, or a protected derivative thereof, or oxo); and R 20 is cyano, -(CH 2 2 S() 2 R 2 -(CH2) 2 C(O)OR 10 -(CH 2 2 P(O)(OR'0)2, 20 -(CH 2 2 S(O)(NRI)R 10 -(CH 2 2 C(O)R 1 1 -(CH 2 2 S(O)R -(CH 2 2 C(O)NR 1 2 R 13 -(CH 2 2 S(0) 2 NR 12 R 13 -(CH2)2C(O)NHR 4 or -(CH) 2 S(O) 2 NHR 1 4 wherein R 2 is I hydrogen, alkyl (optionally substituted with one or more radicals selected from amino, halo, hydroxy, alkyloxy, nitro, alkylsulfonyl and arylsulfonyl, or a protected derivative thereof), cycloalkyl, cycloalkylalkyl or a group selected from aryl and arylalkyl (which group is 25 optionally substituted at its aryl ring with one to two radicals selected from amino, halo, hydroxy, optionally halo-substituted alkyl, alkyloxy, nitro, alkylsulfonyl and arylsulfonyl, or a protected derivative thereof), each R 10 is independently hydrogen, alkyl (optionally substituted with one or more radicals selected from amino, halo, hydroxy, alkyloxy, nitro, alkylsulfonyl and arylsulfonyl, or a protected derivative thereof), cycloalkyl, cycloalkylalkyl i7'- 30 or a group selected from aryl and arylalkyl (which group is optionally substituted at its aryl ring with one to two radicals selected from amino, halo, hydroxy, optionally halo-substituted P:\OPER\DCD\53674-96.215 3/8/99 alkyl, alkyloxy, nitro, alkylsulfonyl and arylsulfonyl, or a protected derivative thereof), R 11 is hydrogen, alkyl, perfluoroalkyl, cycloalkyl, cycloalkylalkyl, perfluoroaryl, perfluoroarylakyl or a group selected from aryl and arylalkyl (which group is optionally substituted at its aryl ring with one to two radicals selected from amino, halo, hydroxy, optionally halo-substituted alkyl, alkyloxy, nitro, alkylsulfonyl and arylsulfonyl, or a protected derivative thereof), R 1 2 and R 13 are independently hydrogen, alkyl, cycloalkyl, cycloalkylalkyl, aryl or aralkyl and R 14 is -C(O)OR' 1 in which R 1 0 is as defined above, or a group selected from Formula and 0 o I (b) wherein each n, A, B, Y, Z, R' and R 1 0 are as defined above; and the pharmaceutically acceptable salts, individual isomers and mixtures of isomers thereof; which process comprises: reacting an aldehyde of Formula XII: S 20 R 8 S* :R210 P RCHO R1 P R XIII XIV in which each R8 and R20 are as defined above and R21 is an alkyl group, and then deprotecting to give a compound of Formula XV: 5 22 o R2 _I P:\OPER\DCD\53674-96.215 3/8/99 -86- R 8 H 2 N )R 20 XV reacting the compound of Formula XV with a compound of Formula VI: o R ZB.A Z'A Z OH 1/n VI in which each n, A, B, Y, Z and R 1 are as defined above, and reducing; optionally further converting a non-salt form of a compound of Formula IV into a pharmaceutically acceptable salt; optionally further converting a salt form of a compund of Formula IV into non-salt form; and 20 optionally further separating a compound of Formula IV into individual stereoisomers.

39. A process for the preparation of a compound of Formula IV: R :R BZA Z1 N in which: n is 0 to 12; SA-B represents a linkage selected from -C(O)NR 3 -CH 2 NR 3 -C(O)CH 2 and P:\OPER\DCD\53674-96.215 3/8/99

87- -NR 3 wherein R 3 is hydrogen or as defined below; Y is -CH(R 5 or -N(R 5 wherein R 5 is hydrogen or as defined below; Z is -(CH 2 2 -C(R 6 )(R 7 or -N(R 7 wherein R 6 is hydrogen or methyl and R7 is as defined below; Z' is -(CH2 2 -C(R 6 )(R 8 or -N(R 8 wherein R 6 is hydrogen or methyl and R 8 is as defined below; R 6 is hydrogen or methyl and R 7 is as defined below; R 1 is hydrogen, alkyloxycarbonylalkanoyl, alkyloxycarbonyl, alkanoyl (optionally substituted with a radical selected from carboxy, alkyloxycarbonyl and heterocycloalkylalkanoylamlno), cycloalkyicarbonyl, neterocycloalkylcaroonyl (optionally substituted with a radical selected from hydroxy, alkyl, alkanoyl, alkyloxycarbonyl, arylalkyloxycarbonyl and heterocycloalkylcarbonyl), arylalkyloxycarbonyl, carbamoyl, alkylcarbamoyl, dialkylcarbamoyl, arylcarbamoyl, arylalkylcarbamoyl, arylalkanoyl, aroyl, alkylsulfonyl, dialkylaminosulfonyl, arylsulfonyl or heteroarylsulfonyl; R 7 and R 8 are independently hydrogen, alkyl (optionally substituted with a radical selected from hydroxy, amino, alkylamino, dialkylamino, uriedo, mercapto, alkylthio, carboxy, carbamoyl, alkylcarbamoyl, dialkylcarbamoyl, alkylsulfonyl and guanidino, or a protected derivative thereof), cycloalkyl, cycloalkylalkyl, heteroaryl, heteroarylalkyl, a group selected from aryl and arylalkyl (which group is optionally substituted at its aryl ring with 20 one to three radicals selected from hydroxy, amino, halo, optionally halo-substituted alkyl, alkyloxy and aryl, or a protected derivative thereof) or together with an adjacent R 3 or R forms a divalent radical selected from a divalent radical selected from (C 3 4 )methylene and 1 ,2-phenylenedimethylene (which radical is optionally substituted with hydroxy, or a protected derivative thereof, or oxo); and R 20 is -CH 2 CHR 1 5 R 6 wherein R'S is hydrogen, methyl, fluoro or a group selected from Formulae (a)and A B 0 P:\OPER\DCD\53674-96.215 5/8/99 -88- wherein each n, A, B, Y, Z, R' and R 10 are as defined above, and R' 6 is a group selected from phenyl or (C 5 -6)heteroaryl (which group is optionally substituted with at least one radical selected from alkylcarbamoyl, dialkylcarbamoyl, alkyloxycarbonyl, alkylsulfinamoyl, dialkylsulfinamoyl, alkylsulfonyl, carboxy, nitro, sulfinamoyl, sulfo, carbamoyl, phosphono, alkyloxyphosphinyl, dialkyloxyphosphinyl, alkanoyl, cyano, alkylsulfinyl, sulfamoyl, alkylsulfamoyl, dialkylsulfamoyl, alkyloxysulfonyl, alkylsulfonimidoyl, aryl, heteroaryl, hydroxy, alkyloxy, optionally halo-substituted alkyl, arylalkyl, halo, -fN(R 1 7 3 wherein each R' 7 is independently alkyl, aryl or arylalkyl, or -N(R' 8 2 wherein each R 18 is independently hydrogen, alkyl, aryl or arylalkyl); and the pharmaceutically acceptable salts, individual isomers and mixtures of isomers thereof; which process comprises: reacting an aldehyde of Formula XII: R PHN CHO with compound of Formula XVI: P(Ph) R6 XVI in which each R 8 R 15 and R1 6 are as defined above, and then deprotecting to give a compound of Formula XVII: 25 R 8 *16 NH 2 R XVII reacting the compound of Formula XVII with a compound of Formula VI: I P:\OPER\DCD\53674-96.215 -5/8/99 -89- R Z B A Z OH VI in which each n, A, B, Y, Z and R' are as defined above, and reducing; optionally further converting a non-salt form of a compound of Formula IV into a pharmaceutically acceptable salt; optionally further converting a salt form of a compund of Formula IV into non-salt form; and optionally further separating a compound of Formula IV into individual stereoisomers. 40. Use of a cysteine protease inhibitor of Formulae I, II, or III in the manufacture of a medicament for the treatment of a cysteine-protease associated disorder. 41. Use of a cysteine protease inhibitor according to any one of claims 1, 13 or 23 in the manufacture of a medicament for the treatment of a condition capable of amelioration 4 20 by the inhibition of a cysteine protease. 42. Method for the treatment of a cysteine protease associated disorder comprising the step of administering to an animal in need thereof an effective amount of a cysteine protease inhibitor of Formulae I, II or III. I P:AOPER\DCD53674-96.215 6/8/99 43. A cysteine protease inhibitor according to any one of claims 1, 13 or 23 substantially as hereinbefore described with reference to the Examples. DATED this 5TH day of AUGUST, 1999 ARRIS PHARMACEUTICAL CORPORATION by DAVIES COLLISON CAVE Patent Attorneys for the applicant(s)