CA2329712A1 - Cysteine protease inhibitors - Google Patents

Abstract

The present invention relates to cysteine protease inhibitors of general formula (I) wherein Z is a cysteine protease binding moiety; X and Y are S, O
or optionally substituted N; and R1 is optionally substituted alkyl or aryl.

Description

CYSTEINE PROTEASE INHIBITORS
Bac ,ground of the Invention Numerous cysteine pretenses have been identified in biological systems. A
"protease" is an enzyme which degrades proteins or peptides into smaller components. The term "cysteine protease" refers to pretenses which are distinguished by the presence of a cysteine residue which plays a critical rale in the catalytic process. Mammalian systems, including humans, normally degrade and process proteins via a variety of mechanisms including the actions of cysteine pretenses. However, when present at elevated levels or when abnormally activated, or where introduced into a biological system in the context of a viral, bacterial or parasitic infection, cysteine pretenses are thought to be involved in numerous pathophysiological processes and disease states.
For example, calcium-activated neutral pretenses ("calpains") comprise a family of intracellular cysteine pretenses which are ubiquitously expressed in mammalian tissues. Three major calpains have been identified: calpain I and II, and p94. The calpain family of cysteine pretenses has been implicated in many diseases and disorders, including stroke, neurodegeneration, such as Alzheimer's disease, amyotrophy and motor neuron damage; acute central nervous system injury, muscular dystrophy, bone resorption, platelet aggregation, cataracts and inflammation. Calpain I has been implicated in excitatory amino-acid induced neurotoxicity disorders including ischemia, hypoglycemia and epilepsy. The cysteine protease p94, a muscle-specific member of the calpain family, has been identified as a gene product responsible.for limb girdle muscular dystrophy (Barrett A.J., et al. ICOP
Newsletter, 1-2 (1996)).
Lysosomxl cysteine pretenses or cathepsins (including cathepsins B, C, H, L, S, O and 02/K) belong to the papain superfamily of cysteine pretenses. They are widely distributed and differentially expressed among tissues. Intracellularly, they serve a variety of digestive and processing functions. Extracellularly, they may be involved in tissue remodeling and in pathologies such as arthritis, inflammation, myocardial infarction, Alzheimer's disease, cancer and muscular dystrophy (Elliott E., et al., Per. in Drug Disc. and Des., 6: 12-32 (1996)).
Interleukin-1 (3 converting enzyme ("ICE'S is a member of the caspase family of cysteine pretenses which catalyzes the formation of interleukin-1 p (IL-1 (i), as well as the formation of WO 99/54317 PCTNS99/0$501 interferon-y inducing factor (IGIF) from their inactive precursors, proIL-1 ~3 and pro-IGIF, respectively. Interleukin-lei is an immunoregulatory protein implicated in inflammation, diabetes, septic shock, rheumatoid arthritis and Alzheimer's disease. ICE
and/or other caspases have also been linked to the apoptotic cell death of neurons which is implicated in a variety of neurodegenerative disorders including Parkinson's disease, ischemia and amyotrophic lateral sclerosis (ALS)(Dinarello C., et al., New Eng. J. Med, 328: 106-113 (1993)).
Cysteine proteases are also produced by various viral pathogens and appear to be involved in every stage of reproduction including DNA and RNA translation and synthesis, and capsid formation (Gorbalenya A., et al., Per. In Drug Disc., 6:64-86 (1996);
Krausslich et al., Ann. Rev. Biochem., 57:701-54 (1988)). Examples of viral pathogens include Picornaviridae, which includes the genera Enterovirus, Rhinovirus, Cardiovirus, and Aphthovirus, which cause numerous human disease syndromes, ranging from fatal paralysis, encephalitis, meningitis, hepatitis and myocarditis to the common cold (Krausslich et al., Ann. Rev.
Biochem., 57:701-54 (1988)). The picornaviral 3C proteinases, which are produced by all picornaviruses, are responsible for processing viral polyproteins, an essential stage in viral growth (Malcolm B., et al. Biochemistry, 34:8172-8179 (1995)).
In addition, parasitic cysteine proteinases play significant roles in host-parasite interactions and pathogenesis (Robertson C., et al., Pers. in Drug Disc. and Des., 6:99-118 (1996)). For example, most of the proteinase activity detected in trypanosomes and various Leishmania species has been characterized as belonging to the cysteine protease class. Other proteases are produced by Clostridium histolyticum and malaria parasites, such as Plasmodium falciparum and Plasmodium vinckei strains, and Schistosoma.
Cancer procoagulant, CP, a cysteine proteinase from malignant cells, has emerged as a probable activator of the coagulation system in cancer (Alessio M.G., et al., Eur. J. Haematol, 45: 78-81 (1990); Gordon S., Methods in Enz., 244:568-581 (1994); Gordon S., Sem. in Thromb.
and Hemo., 18, 4:424-433 (1992)).
Existing cysteine protease inhibitors are primarily irreversible in nature;
only weakly inhibit the enzymatic activity of the targeted protease and/or are toxic.
Thus, there is a need for effective inhibitors of cysteine proteases as therapeutic and as prophylactic agents for the treatment and/or prevention of cysteine protease mediated pathologies.
Summary ref the Invention The present invention relates to cysteine protease inhibitors of the general formula (I):
N-Y
Z~X~Ri (I) wherein Z is a cysteine protease binding moiety, Z being a carbonyl containing group, preferably an amino carbonyl containing group, wherein the carbon of the heterocycle is attached directly to the carbonyl group of Z.
In the above formula (I), R, is alkyl or alkenyl optionally substituted with 1-3 halo or hydroxy; alkylamino, dialkylamino, alkyldialkylamino; or cycloalkyl, alkylcycloalkyl, alkenylcycloalkyl, (Cs-C,~aryl, (Cs-C,~arylalkyl or (Cs-C,Z)arylalkenyl optionally comprising 1-4 heteroatoms selected from N, O and S, and optionally substituted with halo, cyano, vitro, haloalkyl, amino, aminoalkyl, dialkylamino, alkyl, alkenyl, alkynyl, alkoxy, haloalkoxy, carboxyl, carboalkoxy, alkylcarboxamide, (Cs-C6)aryl, -O-(Cs-C6)aryl, arylcarboxamide, alkylthio or haloalkylthio; and X and Y are independently O, S or N, where N is optionally substituted with alkyl or alkenyl optionally substituted with 1-3 halo atoms; (Cs-C6)aryl, arylalkyl or arylalkenyl optionally comprising 1-3 heteroatoms selected from N, O and S, and optionally substituted with halo, cyano, vitro, haloallcyl, amino, aminoalkyl, diallcylamino, alkyl, alkenyl, alkynyl, alkoxy, haloalkoxy, carboxyl, carboalkoxy, alkylcarboxamide, arylcarboxamide, alkylthio or haloalkylthio; provided that at least one of Y or X is N. It will be understood that where Y or X
is substituted nitrogen, both Y and X must be nitrogen.
In one embodiment, R, is methyl, dimethylamino, phenyl or benzyl optionally substituted with methyl, halo, methylenedioxy, methoxy, dimethoxy, trimethoxy, trifluoromethyl and dimethylamino.

WO 99/54317 PC'T/US99/08501 According to severai preferred embodiments, X is O and Y is N; X is N and Y is O; or both X and Y are N.
Typically Z comprises 1 to 5 amino acid residues or mimetics thereof. Thus, Z
may, for example, comprise a pentapeptidyl, tetrapeptidyl, tripeptidyl or dipeptidyl binding moiety.
According to a preferred embodiment, Z is of the formula (II):
R' 4 \
~5-'~4'~3-~2-~' I' (II) wherein AA,, AAA, AA3, AA, and AAs are independently an amino acid residue or amino acid residue mimetic; a direct bond or absent; and R, and R,' are independently -C(O)Rs, -C(O)NHRs, -S(O)iRs, -C(O)OR,, -CR, or Rs, where Rs is H, alkyl, alkenyl or alkynyl optionally substituted with halo, cyano, vitro, haloalkyl, amino, aminoalkyl, dialkylamino, haloalkoxy, carboxyl, carboalkoxy or alkylcarboxamide;
cycloalkyl, alkyicycloalkyl, (Cs-C,Z) aryl or (Cs-C,2}arylalkyl optionally comprising 1-4 heteroatoms selected from N, O and S, and optionally substituted with halo, cyano, vitro, haloalkyl, amino, aminoalkyl, dialkylamino, haloalkoxy, carboxyl, carboalkoxy, alkylcarboxamide, alkyl, alkenyl; alkynyl or (Cs-C,Z)aryl; or absent; or together R, and R4' form a ring comprising 5-7 atoms selected from C, N, S and O. Typical terminal R, groups include Cbz, succinic acid derivatives of the formulas -C(O)CH(-CHZCH(CH3)~CHZCOOH, -C(O)CHiCHiCOOH, and -C(O)CHZCHZC(O)OC(CH~)3; toluenesulfonyl, methane sulfonyl, FMOC, (t)-menthyloxy-CO- aad acetyl.
Preferably, the amino acids are selected from arginine or an arginine mimetic, proline;
aspartic and glutamic acid and the aryl and alkyl esters thereof; alanine and glycine optionally substituted at the a-carbon or a-nitrogen with alkyl, cycloalkyl or aryl;
leucine, isoleucine;
cysteine optionally substituted at the sulfur atom with alkyl, alkenyl or phenyl optionally substituted with halo, cyano, vitro, haloallcyl, amino, aminoalkyl, dialkylamino, alkyl, alkoxy, haloalkoxy, carboxyl, carboalkoxy, alkylcarboxamide, arylcarboxamide, alkylthio or haloalkylthio; phenylalanine, homo-phenylalanine, dehydro-phenylalanine, indoline-2-carboxylic acid; tetrahydroisoquinoline-2-carboxylic acid optionally substituted with halo, cyano, vitro, haloalkyl, amino, aminoalkyl, dialkylamino, alkyl, alkoxy, haloalkoxy, carboxyl, carboalkoxy, alkylcarboxamide, arylcarboxamide, alkylthio or haloallcylthio; tyrosine, serine or threonine optionally substituted with alkyl or aryl; tryptophan, histidine, methionine, valine, norvaline, norleucine, octahydroindole-2-carboxylic acid; asparagine, glutamine and lysine optionally substituted at the nitrogen atom with alkyl, alkenyl, alkynyl, alkoxyalkyl, alkylthioalkyl, alkylaminoalkyl, dialkylaminoalkyl, carboxyalkyl, alkoxycarbonyl alkyl or cycloalkyl, I O bicycloalkyl, cycloalkyl alkyl, bicycloalkyl alkyl or fused aryl-cycloalkyl alkyl optionally comprising 1 or more heteroatoms selected from N, O and S.
Alternatively, AA, is of the formula (IIIa):
N
O

(IIIa) wherein X' is CRZ' or N; and R2, Rz' and R~" are independently H; alkyl or alkenyl optionally substituted with 1-3 halo, hydroxy, thin, allcylthio, amino, alkylamino, dialkylamino, alkylguanidinyl, dialkylguanidinyl, guanidinyl; -RCOR', -RCOOR', -RNR'R"R° or -RC(O)NR'R" where R is alkyl or alkenyl, and R', R" and R° are independently H, alkyl, alkenyl, cycloalkyl or (Cs-C6)aryl; or cycloalkyl, alkylcycloalkyl, alkenylcycloalkyl, alkyl-oxyaryl, alkyl-thioaryl, (Cs-C,2) aryl, (Cs-C,Z)arylalkyl or (Cs-C,~arylalkenyl optionally comprising 1-4 heteroatoms selected from N, O and S, and optionally substituted with hydroxy, halo, cyano, vitro, haloalkyl, amino, aminoalkyl, dialkylamino, amidine, alkylamidine, dialkylamidine, alkyl, alkenyl, alkynyl, alkoxy, haloalkoxy, carboxyl, carboalkoxy, alkylcarboxamide, (Cs-Cs)aryl, -O-(Cs-C6)aryl, arylcarboxamide, alkylthio or haloalkylthio; or RZ and R2' together with X' form a ring comprising 4-7 atoms selected from C, N, S and O, said ring optionally subsitituted with hydroxy, halo, cyano, vitro, haloalkyl, amino, aminoalkyl, dialkylamino, amidine, alkylamidine, dialkyl amidine, alkyl, alkenyl, alkynyl, alkoxy, haloalkoxy, carboxyl, carboalkoxy, alkylcarboxamide, (Cs-C6)aryl, -O-(Cs-C6)aryl, arylcarboxamide, alkylthio or haloalkylthio.
AA2 may be a residue of the formula (IIIb):

N~
R.,3 O
(IIIb) IS or selected from a residue mimetic of formulas IV to XXIV:

i 6 R6 I ..W N~.
( " ''~ n ,Y )m w' 0 N )m N I N.X»
Q O
p O ~ R3 (IV) (~ (vl) v I O i I N~ O N~ O
~. N.X,.X
p ~ I
O ~ R3 O R
(VIII) (1X) (VII) 3 R6 O R6. R7 0 R,6 R
( "W~ O 7wN~ O R,7 O
N'X»~N~X» G~N~N~X»
!II
O R O I O I
R
(7C) 3 (7u) R3 (XII) 3 R'7 ~~ O V1~ y~ O V )" \N 1 /
I X» U N
G~N N,X,~ ~ O

O I 3 Ol (7CIII) R3 (XIV) (XV) (7CVI) _ R6 ~ / ~
\ / ~ \ I R6 O N
N R3 R3. ~ /
N ~'N~X/ N~X/ N O
'~ O X
(XVII) O (XViI1) 0 \ / \ I O / ~
N R N O
N,X/R3 ~N~X~ 3 I N'X»N~NwX»
'IO

(X7q)0 (X)QI) (X?QII) 3 (7CXIV) ~3 wherein X" is CR'3 or N;
R3, R', and R"3 are independently H; alkyl or alkenyl optionally substituted with 1-3 halo, hydroxy, thio, alkylthio, amino, alkylamino, dialkylamino, alkylguanidinyl, dialkylguanidinyl, guanidinyl; -RCOR', -RCOOR' or -RC(O)NR'R" where R is alkyl or alke~nyl, and R' and R" are independently H, alkyl, alkenyl, cycloalkyl or {Cs-C6)aryl;
or cycloalkyl, alkylcycloalkyl, alkenylcycloalkyl, alkyl-oxyaryl, alkyl-thioaryl, (Cs-C,2) aryl, (CS-C,i)arylalkyl or (Cs-C,Z)arylalkenyl optionally comprising 1-4 heteroatoms selected from N, O and S, and optionally substituted with hydroxy, halo, cyano, vitro, haloalkyl, anuno, aminoalkyl, dialkylamino, amidine, alkylamidine, dialkylamidine, alkyl, alkenyl, alkynyl, alkoxy, haloalkoxy, carboxyl, carboalkoxy, alkylcarboxamide, (CS-C6)aryl, -O-(Cs-C6)aryl, arylcarboxamide, alkylthio or halaalkylthio;
m is 0, 1 or 2;
n is 0, 1 or 2;
G is -C(O)-, -NHC(O)-, -S{O)2-, -OC{O)-, -C- or a direct bond;
R6, R,, R'6, R'~ are independently H, alkyl, alkenyl, halo, alkoxy, carboxyl, carboallcoxy, amino, aminoalkyl, dialkylamino; cycloalkyl, (Cs-C6) aryl or (Cs-C6) arylalkyl optionally comprising 1-3 heteroatoms selected from N, O and S, and optionally substituted with alkyl, alkenyl, alkynyl, halo, cyano, vitro, haloalkyl, haloalkoxy, amino, alkylamino, dialkylamino, alkoxy, haloalkoxy, carboxyl, carboalkoxy, alkylcarboxamide, alkyithio, guanidine, alkylguanidine, dialkylguanidine, amidine, alkylamidine or dialkylamidine; and U, V, W and Y' are independently or together N, C, C(O), N(Rg) where R.g is H, alkyl, halo, alkoxy, carboalkoxy, cycloalkoxy, carboxyl, alkylthio, amino, alkylamino, dialkylamino, or aryl, fused aryl or cycloalkyl optionally comprising 1 or more heteroatoms selected from O, S
and N, and optionally subsituted with halo or alkyl; N(R,o) where R,o is H, alkyl, alkenyl or cycloallcyl, aryl, arylalkyl or fused aryl-cycloallcyl optionally comprising 1-4 heteroatom~
selected from N, O and S, and optionally substituted with alkyl, alkenyl, alkynyl, halo, cyano, vitro, haloalkyl, haloalkoxy, amino, alkylamino, diatkylamino, alkoxy, haloalkoxy, carboxyl, carboalkoxy, alkylcarboxamide, alkylthio, guanidine, alkylguanidine, dialkylguanidine, amidine, alkylamidine or dialkylamidine; or C(R")(R,~ where R" and R,2 are independently or together H, alkyl, alkythio, alkythioalkyl or cycloalkyl, alkylcycloalkyl, phenyl or phenyl alkyl optionally subsituted with guanidine, carboalkoxy, hydroxy, haloalkyl, alkylthio, aikylguanidine, dialkylguanidine, amidine, alkylamidine or dialkylamidine.
In a preferred embodiment, X' and X" are C, and R'Z and R'3 are H.
In another embodiment, X' and/or X" are N.
Where Z is a calpain binding moiety, preferably R~ is benzyl optionally substituted with alkoxy; HzNC(--'NH2)NHCHzCH2CHZ-; -R'-C(=+NHZ)NHZ; -R'-NHC(--'NR")NR°;
or -R'-NR"R° where R' is cycloalkyl, aryl or arylalkyl optionally substituted with one or more heteroatoms selected from N, S or O; and R" and R° are alkyl or cycloalkyi; or CH3SCHzCH2-, HOOC(CHz),CH2-, cyclohexyl-CHZ-, imidazolyl-CHZ, benzyl optionally substituted with OH or -O-benzyl, _(CH,)iCHCHz-, (CH,)zCH-, CH3CHZCHZ- or CH3(CHZ)~CHz-; and R, is -CH,-benzyl, benzyl, (CH,),C-, (CH3),CCHZ-, (CH3)ZCH-, CH~(CHZ)ZCHZ-, CH~CHzCH(CH3)- or (CH3)zCHCH,-. Preferably, Rs is benzyl, isoquinolinyl, quinolinyl, naphthyl or HOOCCH~C(CH~CH(CH3)Z)-; or R, is Cbz wherein the phenyl is optionally substituted with vitro. Additionally, R, may be toluenesulfonyl, methanesulfonyl, FMOC or (+)-menthyl-oxy-CO-.
In one embodiment, AA3 is leucine, AA4 and AA3 are direct bonds or absent, and Rs is alkyl.
Several particular embodiments include those where Z is R~-Leu-Leu-Leu-R4-Leu-Leu-;
R,~Leu-Leu-Phe-;
R,-Leu-Abu-;
R4-Val-Phe-;
R,-Leu-Leu-Nle-;
R,-Ala-t-BuGly-Val-R~-t-BuGly-Val-R~-Leu-Leu-Met-; or R,-Leu-Nle-.

Preferably, Z is Cbz-Leu-Nle-; or Cbz-Leu-Val-.
Z may also be a cysteine cathepsin binding moiety, where preferably RZ is CHI-, (CH3)ZCH-, (CH,)zCHCHz-, CH,(CHz)ZCHz-, HZNC(--'NHZ)NHCH~CHZCHz-; -R'-C(--'NHZ)NHz; -R'-NHC(='NR")NR°; or -R'-NR"R° where R' is cycloalkyl, aryl or arylallcyl S optionally substituted with one or more heteroatoms selected from N, S or O;
and R" and R° are alkyl or cycloalkyl; benzyl or -CHZ-benzyl optionally substituted with OH or -OR' where R' is alkyl or aryl; CH,CH(-O-benzyl)- or benzyl-S-CHi-; and R, is H, (CH3)iCH-, (CH3)iCHCHZ-, CH,(CHZ)zCH2-, HZN{CH~)3CH~-, H,N(CH2)zCH~-, HZNC(='NHZ}NHCH2CHZCH2-; -R'-C(='NH,)NH2; -R'-NHC(='NR")NR°; or -R'-NR"R° where R' is cycloalkyl, aryl or arylalkyl optionally substituted with one or more heteroatoms selected from N, S or O;
and R" and R° are alkyl or cycloalkyl; benzyl, benzyl substituted with hydroxy and halo; or (naphthyl)-CHz-.
In one embodiment, Z is a cathepsin B binding moiety, where preferably, RZ and R3 are independently benzyl, -CHZ-benzyl, HzNC(='NHZ)NHCHZCHzCHz-; -R'-C{='NH~NHZ; -R'-NHC(='NR")NR°; or -R'-NR"R° where R' is cycloalkyl, aryl or arylalkyl optionally substituted with one or more heteroatoms selected from N, S or O; and R" and R° are alkyl or cycloalkyl;
H~N(CHZ)3CH~- or HzN(CH~)2CHz-; and preferably AA3 is Ile, Leu, absent or a direct bond.
According to a particular embodiment, -AAZ-AA,- are selected from:
-Phe-hPhe-;
-Arg-hPhe-;
-Arg mimetic-hPhe-;
-Leu-hPhe-; and -Onn-hPhe.
Z may be a cathepsin L binding moiety, where R3 is preferably benzyl or (CH3~CHCHi-;
and R2 is -CHZ-bcnzyl.
Where Z is a cathepsin S binding moiety; preferably RZ and R3 are alkyl; more preferably (CH,)ZCH-, (CH3~CHCHZ- or CH,(CH~ZCHZ-.
In another embodiment, R, is benzyl, (CH3)zCHCHZ- or (CH3~CH-; and R2 is -CHZ-benzyl. According to one particular embodiment, AA3, AA, and AAf are direct bonds or absent;
R, is benzyl, isoquinolinyl, quinolinyl, naphthyl or HOOCCHZC(CHiCH(CH3)2)-;
or R, is Cbz.

Where Z is a cathepsin H binding moiety; Z is preferably R,-hPhe-; or HCl~hPhe-.
Z may also be a cathepsin K binding moiety; where preferably R3 is benzyl, (CH3)zCHCHz- or (CH~~CH-; and preferably AA3 is Gly; and AA, is Val or D-Val.
In another embodiment, AA, is Arg, Arg mimetic or hPhe;
AAZ is Pro;
AA, is Gly; and AA4 is VaI or D-Val; or preferably Z is R,-Pro-AA,-;
R4-Gly-Pro-AA,-;
R4-Val-Gly-Pro-AA,-;
1 S D-Val-Gly-Pro-AA,-; or R,-D-Val-Gly-Pro-AA,; where AA, is Apa, Arg or Arg mimetic, or hPhe.
Other embodiments include compounds where Z is R,,-AA3-Leu-hPhe-;
R,-AAA-Phe-hPhe-; or R,-AA3-Val-hPhe-;
where AA3 is Gly, Val, D-Val, a direct bond or absent.
Where Z is a caspase binding moiety; preferably RZ is -RCOOR'; where preferably R is -CHi- and preferably R' is H; where preferably AAA and AAA are amino acid residues and AAs is a direct bond.
Where Z is an interleulcin-1 ~i converting enzyme binding moiety; AA4 may be optionally substituted tyrosine or leucine; AA, may be valine, glutamate or an ester of glutamate; and R3 may be -CH3 or (CH3)ZCH-.
In another embodiment, R3 is -CH3 or imidazolyl-CH2-; AA3 is valine or glutamate; and R, is -CHI.
Z may also be Ry-AAS-AA4 AAA-Pro-AA,; where AA, is Asp or Asp ester; where -AAs-AA,-AA,- may be -Ala-; -Glu-; -Val-; -Tyr-Ala-; -Tyr-Glu-; -Tyr-Val-; -Leu-Ala-; -Leu-GIu-; or -Leu-Val-.
In yet a further embodiment where Z is an interleukin-1 p converting enzyme binding moiety, AA, is of the formula (VI);
wherein X" is CR'3 where preferably R'3 is H; and R, is -RCOOR' where R is alkyl or alkenyl, and R' is H, alkyl, alkenyl, cycloalkyl or (Cs-C6) aryl. In another, AA, and AAs are direct bonds or absent, AA3 is Tyr or Tyr(O-R') or a direct bond or absent; RZ is -RCOOR' where R is alkyl or alkenyl, and R' is H, alkyl, alkenyl, cycloalkyl or (Cs-C6) aryl; R6 is phenyl or benryl substituted with halo; and Rs may be benzyl, isoquinolinyi, quinolinyl, naphthyl or HOOCCHiC(CH,CH(CH3)z)-.
Where Z is a YAMA binding moiety, preferably Rz is -RCOOR' where preferably R
is -CHI- and AA4 is Asp or an ester thereof. In another embodiment, AA3 is optionally substituted glutamine or glutamic acid or an ester thereof. In yet another embodiment RZ
is (CH3)2CH- or CH,SCHzCH2-.
Where Z is a FLICE binding moiety, preferably Ri is -RCOOR', where preferably R is -CHz-; AAQ is optionally substituted lysine; and preferably AA3 is glutamic acid; and R3 is (CH,)ZCH-.
Z may also be a viral or microbial cysteine protease binding moiety. In one embodiment, Z is a gingipain binding moiety. Where Z is a gingipain K binding moiety; RZ
is preferably -RNR'R"R° where preferably R is (C,-C,)alkyl; R' is H; and preferably R" and R° are H or (C,-C~)alkyl. In one embodiment RZ is 'H3N(CHZ)3CH2-. Where Z is a gingipain R
binding moiety, preferably Ri is HzNC(='NH~NHCHZCHZCHz-; -R'-C(=iNH~NHZ; -R'-NHC(=*NR")NR°; or -R'-NR"R° where R' is cycloalkyl, aryl or arylalkyl optionally substituted with one or more heteroatoms selected from N, S or O; and R" and R° are alkyl or cycloalkyl.
According to one embodiment, AAz is proline, where Z is R,-Leu-Pro-AA,-, where AA, is arginine or an arginine mimetic.
Z may also be a human coronavirus protease binding moiety, where preferably Ri is HzNC(='NH~)NHCH~CHzCH2-; -R'-C(='NHZ)NH2; -R'-NHC(='NR")NR°; or -R'-NR"R°
where R' is cycloalkyl, aryl or arylalkyl optionally substituted with one or more heteroatoms selected from N, S or O; and R" and R° are alkyl or cycloalkyl; and preferably R3 is (CH3)zCH-, {CH,)ZCHCH~- or CH3(CHZ)iCHz-; AA3 is Asp or ester thereof, Leu, Arg or Arg mimetic, or direct bond; AA, and AAs are direct bonds or absent; and Rs is alkyl.
Where Z is a hepatitis A virus 3C proteinase binding moiety, RZ is preferably -RC(O)NR'R" where R' and R" are H or -CH,; or RCOOR' where R' is CH,; and AAA
and AA4 are amino acid residues. Preferably, AA4 is Leu; R~ is -CH3 and AA3 is Ala.
Z may also be a hepatitis A virus 3C proteinase binding moiety, where Z is R4-Leu-AA3-Thr-Gln-;
R,-Trp-AA3-Thr-Gln-;
R4-Val-AA3-Thr-Gln-;
R,-Ile-AA,-Thr-Gln-; or R~-D-Leu-AA,-Thr-Gln-;
where AA3 is Arg or Arg mimetic.
Where Z is an Ad2 23K protease binding moiety, RZ and R3 are preferably H; AA3 is alanine; AA, is leucine; AAs is a direct bond; and R, is absent.
Where Z is a human rhinovirus 3C protease binding moiety, preferably RZ is RCOOR' where R is -CHi-; R3 is benzyl; and AA3 is leucine, isoleucine or a direct bond.
In yet a further embodiment, RZ is -RC(O)NR'R" where R' and R" are H, -CH3 or -CHZCH3; or RCOOR' where R' is -CH; or -CHzCH3.
Z may also be a human picornain 2A protease; where R3 is -CH(OR')CH3 where R' is H, alkyl or aryl; and preferably Ri is a hydrophobic side chain. Alternatively, AA, is Val or dehydro-Phe; AAz is Pro; and AA3 is Val. Examples include compounds CE-2072, CE-2060 and CE-2061, the structures of which are shown below.
In another embodiment, Z is R4-Ala-Ala-Pro-Val-; or R,-Ala-Ala-Pro-Ala-.
Additionally, Z may be a protozoan protease binding moiety, such as a Trypanosoma, Leishmania or Schistosoma protease binding moiety. The protease may be a cathepsin L- or cathepsin B-like protease. In one embodiment, Rz is HZN(CHZ)3CHi-, HZNC(=TNH,)NHCHZCH2CHz-; -R'-C{--'NHZ)NH2; -R'-NHC(--+NR")NR°; or -R'-NR"R°
where R' is cycloalkyl, aryl or arylalkyl optionally substituted with one or more heteroatoms selected from N, S or O; and R" and R° are alkyl or cycloalkyl; -CH,-benzyl or benzyl optionally substituted with OH; and preferably R, is benzyl, (CH3)ZCHCHZ- or (CH3)ZCH-; and AA3 is Phe, Leu, Pro or a direct bond. In one example, R, is Boc or Suc.
Z may be also selected from -Pro-Phe-Arg-; -Phe-Arg-;-Val-Leu-Lys-; -Leu-Val-Tyr-;
Suc-Leu-Tyr- or -Phe-Ala-.
Where Z is a Plasmodium protease binding moiety, preferably R2 is (CH~)iCH-, -CHZ-benzyl, benzyl or phenyl optionally substituted with hydroxyl; HZNC(--'NHZ)NHCHzCHzCH2-;
-R'-C(--'NHz)NH=; -R'-NHC(--'NR")NR°; or -R'-NR"R° where R' is cycloalkyl, aryl or arylalkyl optionally substituted with one or more heteroatoms selected from N, S or O; and R"
and R° are alkyl or cycloalkyl; or -R'-N(R")(R°) where R' is alkyl, and R" and R° are alkyl or cycloalkyl; or alkylimidazoyi; and R3 is benzyl, (CH3)ZCHCHz-, (CH,)ZCH-, HOCHz- or -CH20R'.
In one embodiment, Z is R,-Phe-Arg-;
R,-Phe-(arginine mimetic)-;
R4-Phe-Lys-;
R,-Leu-hPhe-;
R,,-Val-Leu-Arg-;
R4-Phe(e-Z)-Lys-;
R,-Val-Leu-(Arg mimetic)-R,-Phe-Val-; or R,-Phe-Ser(OBzI)-.
In another embodiment, Z is R,-Phe-AA,-; or R,-Leu-AA,-;

where AA, is optionally substituted lysine; and where R, may be morpholino. In a further embodiment, AA3, AA4 and AAs are direct bonds or absent, and R, is Cbz.
The present invention also provides methods of inhibiting the enzymatic activity of one or more cysteine proteases comprising contacting a protease with an inhibitory amount of a compound described herein.
Preferably the compound is selected from [2-[5-(3-methylbenzyl)-1,3,4-oxadiazolyl]carbonyl]-2-(S)-methylpropyl]-L-phenylalanamide-(3R)-(isobutyl)succinic acid;
Acetyl-L-leucyl-N-[1-[2-[5-phenyl]-1,3,4-oxadiazolyl]carbonyl]-4-(guanidino)-butyl-L-leucyl amide;
Acetyl-L-leucyl-N-[1-[3-[5-methyl]-1,2,4-oxadiazolyl]carbonyl]-ethyl-L-leucyl amide;
Acetyl-L-leucyl-N-[1-[3-[5-methyl]-1,2,4-oxadiazolyl]carbonyl]-4-(guanidino)-butyl-L-leucyl amide;
Acetyl-L-tyrosinyl-L-valyl-N-[1-[2-[(5-phenyl)-1,3,4-oxadiazolyl]carbonyl]-2-carboxy-ethyl]-L-alanine amide;
Acetyl-L-Aspartyl-Valyl-N-[1-[2-[(5-phenyl)-1,3,4-oxadiazolyI] carbonyl]-2-(carboxy)-ethyl]-L-glutamyl amide;
(Benzyloxycarbonyl)-L-valyl-N-[I-(2-[5-(3-methylbenzyl)_1,3,4-oxadiazolyl]carbonyl)-2-(S)-methylpropyl]-L-prolinamide;
(t-butoxysuccinyl)-L-valyl N-[1-[3-[5-(3-trilluoromethylbenzyl)-1,2,4-oxadiazolyl]carbonyl]-2-benzylidone]-L-prolinamide; and Carboxysuccinyl-L-valyl-N-[1-[3-[5-(3-trifluoromethylbenzyl)-1,2,4-oxadiazolyl]carbonyl]-2-benzylidone]-L-prolinamide.
The present invention also provides a method of inhibiting cancer cell growth or tumor progression or tumor metastasis or invasion, by inhibiting the enzymatic activity of cysteine proteases associated with such growth or progression, such as cathepsin B or cathepsin L.
Further provided is a method of inhibiting microbial cell or viral growth or reproduction by inhibiting the enzymatic activity of cysteine proteases associated with such growth or reproduction. Suitable pathogenic targets include, by example only, hepatitis A virus 3C

proteinase, hepatitis C virus endopeptidase 2, piconnain 3C rhinovirus protease, encephalomyelitis virus endopeptidase 2 and picornain 2A protease.
The present invention also provides a method of treating the symptoms associated with allergic responses by inhibiting the enrymatic activity of cysteine proteases associated with certain allergens, such as, for example Der p I.
The invention provides a method of treating the symptoms associated with neurodegenerative disorders, such as Alzheimer's.disease, Parkinson's disease, multiple sclerosis. The invention further provides a method of treating the symptoms associated with stroke.
Further provided is a method of treating the symptoms associated with inflammatory and degenerative diseases, such as arthridities, including rheumatoid arthritis or osteoarthritis, or periodontal disease.
As used herein, the term "cysteine protease binding moiety" means a chemical group capable of binding to the substrate binding site of a cysteine protease, typically defined in the literature as the S,-S" site. The term includes both peptides and peptide mimetics. Preferably, the binding moiety is selected such that when linked to the keto-heterocycle, the moiety provides the resulting compound with inhibitory activity against the target cysteine protease of less than 100 wM (K; value); and more preferably of less than 10 ~M.
As used herein, the term "optionally substituted" means, when substituted, mono to fully substituted.
As used herein, the term "independently" means that the substituents may be the same ar different.
As used herein, the term "alkyl" means C,-C,s, however, preferably C,-C,.
As used herein, the term "alkenyl" means C,-C,s, however, preferably C,-C,.
As used herein, the term "alkynyl" means C,-C,s, however, preferably C,-C.,.
It will be understood that alkyl, alkenyl and alkynyl groups, whether substituted or unsubstituted, may be linear or branched.
As used herein, the term "aryl," unless otherwise stated, means aryl groups preferably comprising 5 to 12 carbons, and more preferably 5 to 6 carbons. Unless otherwise indicated, the term aryl includes mono-and bi-cyclic, as well as fused ring systems. As used herein, the term "arylalkyl" includes mono-substituted alkyl groups (e.g., benzyl), as well as di-substituted alkyl groups such as -alkyl(phenyl)z (e.g., -CH(phenyl)Z). As used herein, where the term "arylalkyl"
or "arylalkenyl" is defined by the general formula (Cx Cy)arylalkyl or (Cx CY)arylalkenyl, x and y refer to the number of carbons making up the aryl group. The alkyl group is as defined above.
As used here, the term "arylalkenyl" includes aryl compounds having an alkenyl chain comprising 1-3 or more double bonds. Exemplary arylalekenyl groups include =CH-CHZ-aryl and -CH=CH-aryl, where aryl is preferably phenyl.
As used herein, the term "arginine mimetic" means an amino acid residue with a side chain substituent of the formula -R'-C(--'NH,)NHz; -R'-NHC(--'NR")NR°;
or -R'-NR"R° where R' is cycloalkyl, aryl or arylalkyl optionally substituted with one or more heteroatoms selected from N, S or O; and R" and R° are alkyl or cycloalkyl.
As used herein, the term "Cbz" means benzyloxycarbonyl; and the term "Mu "
means morpholino.
Pharmaceutically acceptable salts of the compounds described above are within the scope of the invention.
Figure 1 shows the inhibition of the production of mature IL-1 p in THP-1 cell line by certain compounds of the present invention.
Figures 2A and 2B show the inhibition of the production of mature IL-1 ~i in whole blood by certain compounds of the present invention.
Figure 3 is a schcmadc representation of the synthesis of a compound according to the invention (CM-0019).
The present invention provides compounds which are useful as cysteine protease inhibitors. These compounds are characterized by their relatively low molecular weight, reversible inhibition, high potency and selectivity with respect to various types of cysteine proteases. The compounds can be implemented to prevent, alleviate and/or otherwise treat diseases which are mediated by the effects associated with the presence of cysteine proteases.
Their usage is of particluar importance as they relate to various human treatments in vivo and as well as diagnostic tools in vitro.
Peptidyl inhibitors of serine proteases comprising serine protease binding moieties and certain keto-heterocycles have been previously described (see WO 96/16080). It has been surprisingly found that compounds comprising cysteine protease binding moieties and these keto-heterocycles are highly potent and specific inhibitors of a wide variety of cysteine proteases as well. The inhibiting activity can be directed against any cysteine protease by identifying the binding moiety specific for that protease. The characteristics for the P, . .
. P~ residues (using substrate nomenclature by Schechter and Berger (Biochem. Biophys. Res. Commun.
27: 157 {1967); Biochem. Biophys. Res. Commun. 32: 898 (1968) ), which define the minimum recognition sequence of enzymes for small synthetic peptide substrates or inhibitors are known for many enzymes or can be determined by measuring rates of hydrolysis of various substrates.
Some examples are listed in Table 1.
Table 1. Cvsteine proteases and exemplary recognition elements.
Cysteine P 1 P2 Other Reference Protease Calpain I large hydrophobicLeu, bulky 18 and II

e.g. Nva, aliphatic, Phe, Abu hPhe Calpain I Arg or Arg- t-butyl-Gly, 38 Leu, mimetic, Vat, hPhe Lys, Tyr, Val, NIe, Tyr(O-Bzl), Leu, Abu, Phe Papain hPhe, Arg bulky, non-polar, 22 or its mimetics, Phe Agly, Aala Cathepsins bulky hydrophobicVal, Leu 18, 21, 22, Cysteine residues like hphe, (in general)Phe, Met, Abu, Nva, or Arg and its m imetics Cathepsin hPhe, Phe, Phe, Arg P3-large 42 B Tyr, or its Ser(OBzI), mimetics, hydrophobic Leu, Tyr, Thr(OBzI), Np2, Lys, aromatic, Ornithine Ile Cys(SBz1), Arg or its mimetics, Gly Cathepsin Val, Nle, Leu, Phe, 42, 43 S hPhe, Phe Val Cathepsin hPhe, Lys Phe, Leu 42 L

Cathepsin Arg or its Pro, Leu, P3 - Leu 44 K mimetics, Phe, Val hPhe, Leu Cathepsin Arg or its H mimetics, hPhe Caspases Asp P4 - determines22, 40 the specificity within the caspase family Interleukin-lAsp P3 - Val, 22, 36, 41, p Glu or 45, 48 converting ester thereof enzyme P4 - Tyr;
Leu Caspase 3 Asp P4 - Lys 40, 41 (YAMA) Caspase 8 Asp Val P3 - Glu 40, 41 (FLICE) P4 - Asp Picomain Gln or its Phe, Gly P3 - Ile 9 derivatives P4 - small (e.g.

dimethylGln, hydrophobic Azogln), residues Glu and its derivatives Human RhinovirusGln or its Phe P3 - Leu 8 3C protease derivatives (e.g.

dimethylGln, Azogln), Glu and its derivatives Hepatitis Gln or its Ala, Val, P3 - Arg 14 A Virus Leu, Nle, or iu 3C proteinasederivativesPhe mimetics, (e.g. Ala dimethylGln, P4 - hydrophobic Azogln); residues Glu and its derivatives Human CoronaArg or its Val, Leu, P3 - Asp 1 mimetics Nle or its Virus protease esters Hepatitis Leu Leu P3 - Arg 8 C Virus or its endopeptidase mimetics Ad2 23K proteaseGly Gly P3 - Ala, 8 P4 - Leu Trypanosome,Arg or its Phe, Leu, P3 - Pro 23 mimetics, Vat ,Val, Leu Leishmania Lys, Tyr, Aia protease Picornain Gln or its Thr, Gly, P3 - Ala 9, 46 2A Pro derivatives (e.g.

dimethylGln, Azogln), Glu and its derivatives, Tyr, Val, Ala Gingipain Lys, Om 30, 47 K

Gingipain Arg or its Pro, Leu P3 - Leu 30 R mimetics Malaria! hPhe, Arg large hydrophobicP3 - Val 23a or its hemoglobinasemimetics, residues, Lys, Val, e.g. Phe, Ser(OBzI), Leu InnNva, Tyr Nva=norvaline; Abu=a-aminobutyric acid; Agly=azaglycyl; Aala=azaalanyl; Np2=2-naphthylalanine; Nle=norleucine; Eps=epoxysuccinyl In addition to altering the binding moiety Z, the substituent on the heterocycle {i.e., R,) can be varied to further increase the specificity of these compounds toward the desired cysteine protease.
By way of example, the compound CM-0019 comprises the binding moiety specific for papain and a substituted 1,3,4-oxadiazole:
w I
0 ~ o H NH N-N

O CH3 O ~CH3 i CH3 w By way of further example, the compounds CQ-0010 and CQ-0011 inhibit caspases.
Compounds CQ-0002 and CQ-0008 are analogs of leupeptin, the structure of which is provided below for comparison.

O / 1CH3 O O ! 'CH O
_ 3 H3 NH NH ~ ~ H3C NH ~ 'NH
NH~ / ~ NH~ H
p CH3 'Of O ~ ~ O CH3 ''O

CQ-0002 NH H Leupeptin NH~
NHx Compounds CQ-0004, 0008, 0010 and 0011 are represented below:

O "CH3 O N_O , OH
H3C NH NH NH y ~ CH
N CH3 O v p 3 O
O CH3 O NH ~ N-N
H3C~NH NH ~ ' /

O CH O O
H3C~ 3 ~O

p CH3 O
N-O
H3C\'NH ~~NH / ~ HO H O
~'N CH3 O O O _ CH3 ~ NH H3 NH NH NH NH
C~.ooo8 ~ O J~ O
H3~ CH3 OH

Other specific inhibitors include compounds CE-2072, CE-2060 and CE-2061, which have shown inhibitory activity against picornain 2A protease (100% inhibition at 100 pM):
' o3C CH H3C CH3 -N
O~NH
O NH O
O
O /

/

O
H3 O ~~ N I N-O
NH /
H3C~ O NH N
CH3 O O o /
1$ CE-2060 CFy O
HO ~ N
i 0 0 ~ N

/

CFy The compounds of the present invention, salts thereof, and their intermediates can be prepared or manufactured as described herein or by various methods known in the chemical art, as well as by extension and modification of methods previously described (see WO 96/16080, incorporated herein by reference).

An alternative method has been used where suitably protected peptides are converted by the action of an activating coupling reagent such as BOP-CI or HBTU to a Weinreb amide. The Weinreb amide is then reacted with a 5-substituted 2-lithio-1,3,4-oxadiazole at appropriate temperatures ranging from -78 °C to ~25 °C in a suitable solvent such as THF or ether to provide the desired keto-oxadiazoles in a single step. Protecting groups, if present, are then removed to provide the enzyme inhibitors in an efficient and convergent manner. A number of effcient methods to synthesize 5-substituted I,3,4-oxadiazoles are known in the art.
Conveniently, these compounds can be synthesized in a single step by refluxing hydrazides of common carboxylic acids with excess ethyl orthoformate at high temperature. The excess orthoformate is hydrolyzed in the workup and the 5-substituted 1,3,4-oxadiazoles are often obtained in essentially pure form without further purification necessary. This entire method of synthesis is illustrated in general form in scheme 1 below. Instances where Rz correlates to the amino acid side chains of aspartic acid, arginine, and alanine are provided in the Examples.
IS
Scheme 1.
o R~ He~ru o R, cH, ~OH 01EA ~ N
AAn N ~'I( ~ AAn N ~OCH~

R~z O H.~.1V+ R~z O
H ~ 1 OCH~
~N~ t. Ethyl orthofarmate o ~R
I Ri Li O 2. n-Bu-Li -78 C
N~--R
AAn N~O
R~z 1fO

where AA" means AAZ . . . AAs.
The compounds described herein are useful in inhibiting the activity of cysteine proteases, by contacting the compound with the targeted protease, either in an in vivo or an in vitro environment. As used herein, the term "contacting" means directly or indirectly causing the inhibitor and the protease to come into physical association with each other.
Contacting thus includes physical acts such as placing the inhibitor and protease together in a container, or administering the inhibitors to a patient. Thus, for example, administering a compound of the invention to a human patient evidencing a disease or disorder associated with abnormal and/or aberrant activity of such proteases in a method for inhibiting the enzymatic activity of such proteases which are associated with disease or disorder, falls within the scope of the definition of the term "contacting."
Pharmaceutically acceptable salts of the cysteine protease inhibitors also fall within the scope of the compounds as disclosed herein. The teen "pharmaceutically acceptable salts" as used herein includes organic and inorganic acid addition salts such as chloride, acetate, maleate, fumarate, tartrate and citrate. Examples of pharmaceutically acceptable metal salts are alkali metal salts such as sodium salt or potassium salt, alkaline earth metal salts such as magnesium salt and calcium salt, aluminum salt and zinc salt. Examples of pharmaceutically acceptable ammonium salts are ammonium salt, trishydroxymethylaminomethane and tetramethylammonium salt. Examples of pharmaceutically acceptable amino acid addition salts are salts with lysine, glycine and phenylalanine.
Cysteine proteases which may be inhibited by the compounds described herein include mammalian, bacterial, parasite, viral, fungal, insect and plant cysteine proteases. Cysteine proteases include papain, actinidain, aleurain (barley), allergen (Dermatophagoides), allergen (Euroglyphus), ananain (Arranas comosus), asclepain (Asepias syriaca), bleomycin hydrolase, calotropin (Calotropis), caricain, clostripain, cathepsin B, cathepsin H, cathepsin L, cathepsin S, cathepsin O, cathepsin K, cathepsin T, chymopain, cysteine aminopeptidase (Lactococcus), cysteine endopeptidases 2 and 3 (barley), cysteine endopeptidases (Brassica napus), cysteine endopeptidase (Caenorhabditis), cysteine endopeptidases 1 and 2 (Dictyostelium), cysteine endopeptidase (Entamoeba), cysteine endopeptidases 1 and 2 (Haemonchus), cysteine endopeptidase (Hemerocallis), cysteine endopeptidases 1, 2 and 3 (Homarus), cysteine endopeptidase (Leishmania), cysteine endopeptidase (mung bean), cysteine endopeptidase (Ostertagia), cysteine endopeptidase (pea), cysteine endopeptidase (Plasmodium), cysteine protease tpr (Porphyromonas), cysteine endopeptidase {Tetrahymena), cysteine endopeptidase (Theileria), cysteine endopeptidase (tobacco), cysteine endopeptidase (Trypanosoma), dipeptidyl peptidase I, endopeptidase (baculovirus ofAutographa), endopeptidase EP-C1 (Phaseolus vulgaris), glycyl endopeptidase, oryzain (includes a, (i and y) (rice), bromelain (including stem-and fruit bromelain), ficin, thaumatopain (Thaumatococcus); gingipain R and gingipain K;
calpains, including calpain (Schistosoma), calpain I, calpain II, calpain p94, calcium-binding protein PMP41, sol gene product (Drosophila); streptopain and cysteine endopeptidase (Porphyromonas); picarnain 2A, picornain 3C, apothovirus endopepiidase, cardiovirus endopeptidase, comovirus endopeptidase, nepovirus endopeptidase; tobacco etch virus NIa endopeptidase, hepatitis C virus endopeptidase 2, adenovirus endopeptidase;
tobacco etch virus HC-proteinase; chestnut blight virus p29 endopeptidase; chestnut blight virus p48 endopeptidase;
sindbis virus nsP2 endopeptidase; mouse hepatitis virus endopeptidase, avian infectious bronchitis virus endopeptidase; a-clostripain; ubiquitin carboxyl-terminal hydrolase;
deubiquinating enzyme (DOA4 protein), ubiquitin-specific processing peptidase 1, ubiquitin-specific processing peptidase 2, ubiquitin-specific processing peptidase 3, tre oncogene protein {human), unp protein (mouse); hemoglobinase (Schistosoma), legumain (jack bean); interleultin converting enzyme and caspases, such as caspase 2 (ICH-1), caspase 3 (CPP32, YAMA), caspase 4 (ICEreI-II), caspase S (ICEreI-III), caspase 6 (Mch2), caspase 7 (Mch3), caspase 8 (FLICE, MchS), caspase 9 (Mch6, ICE-LAP6), caspase 10 (Mch4); pyroglutamyl-peptidase I; microsomal ER60 protein endopeptidase; prepiliii leader peptidase; PRRS arteritis virus PCP a-endopeptidase, equine arteritis virus Nsp2 endopeptidase; foot and mouth disease virus L
proteinase; hepatitis A viral protease; human corona virus protease;
encephalomyelitis virus endopeptidase; malarial hemoglobinase; drosophila hedgehog virus gene product;
dipeptidyl peptidase I (cathepsin C); Der pl (dust mite); y-glutamyl hydrolase; Actinide (Actinidia); yeast cysteine proteinase E, yeast proteinase D, yeast proteinase F; cancer procoagulant; and histolysin. Enzyme inhibitors for cysteine proteases may be useful as potential therapeutic drugs for humans or animals, as diagnostic or research tools, as antibacterial agents, herbicides, fungicides or pesticides. Potential indications for cysteine protease inhibitors described herein, used in prophylaxis, cure or therapy, include:
Cardiovascular disorders--ischemia reperfusion injury from transplantation andlor vascular surgery, angiogenesis, neovascularization, acute cardiac allograft dysfunction, ischemic cardiac damage, chemotherapy-induced myocardial suppression;
Inflammatory disorders - rheumatoid arthritis and other inflammatory arthritidies, inflammatory bowel disease, inflammatory peritonitis, sepsis, systemic inflammatory response syndrome, multiple organ failure;
Musculo-skeletal disorders--osteoarthritis, osteoporosis, muscular dystrophy, myositis;
Neurological disorders-- multiple sclerosis, stroke, Alzheimer's disease, prion-associated disorders, ataxia telangiectasia, central nervous system injury;
Pulmonary disorders-- asthma, COPD, adult respiratory distress syndrome, Wegener's granulomatosis, emphysema;
Allergic, immunologic and autoimmune disorders--house dust mite allergy, transplant rejection, graft verses host disease, Type 1 diabetes mellitus, autoirnmune thyroiditis, psoriasis, antibody-mediated autoimrnune diseases, lupus erythematosus, Sjogren's syndrome, autoimmune encephalomyelitis;
Solid tumors, lymphomas, leukemias and other malignancies and related disorders--acute and chronic myelogenaus leukemia, neuronal cancer, cancer invasion and metastasis, tumor angiogenesis, B and T cell lymphomas, acute and chronic lymphocytic leukemia, resistance to chemotherapy, cancer associated coagulopathies (including deep venous thrombosis, coronary artery disorder, pulmonary embolism, disseminated intravascular coagulation), Hodgkins disease, carcinomas of the colon, liver, lung, breast, kidney, stomach, pancreas, esophagus, oral pharynx, intestine, thyroid, prostate, bladder, brain; osteo-sarcoma, chondro-sarcoma and liposarcoma;
neuroblastoma; melanoma; and carcinomas derived from amnion and/or chorion);
Infectious diseases and associated syndromes--septic shock (including Gram-negative sepsis), HIVinfection and AIDS, genital herpes, zoster, chickenpox, EBV
infections and encephalitis, CMV-choreoretinitis or encephalitis, cytomegalovirus infections in neonates WO 99!54317 PCT/US99/08501 (including related pneumonitis), opportunistic infections in immunocompromised individuals (including AIDS and transplant patients), dysentery, hepatitis C, hepatitis A, keratoconjuctovitis, bronchopneumonia (including pneumonia in immunocompromised individuals), gastroenteritis, malaria, rhinovirus, polio, enterovirus infections, common cold, aseptic meningitis, foot and mouth disease, Klebsiella pneumonia infection, escherichia coli or staphylococcus epidermidis, leprosy bacteremia, otitis media, lambiiasis, non-atopic sinusitis, fulminant hepatitis;
Kidney disorders--polycystic kidney disease, glomerulonephritis;
Other miscellaneous disorders--periodontal disease, alcohol hepatitis, prostate hypertrophy, trauma, cutaneous mastocytosis, radiation- and HIV-induced diarrhea, cachexia (including acompanying cancer and malnutrition).
Examples of cysteine proteases and associated disease are described in Table 2.
Table 2.
Cysteine Protease Disease State References Interleukin 1 (3 Stroke, traumatic Patel, et al., FASEB, convening brain 10:587-enzyme (ICE, Caspaseinjury, organ transplant597 (1996);.
1) rejection and septicBarr et al., BiofTechnology, shock.

Inflammatory disorders12:487-493 (1994);
Epstein, including the arthritides,New Eng. J. Med., such 328:106-as rheumatoid arthritis113 (1993).
and osteoarthritis, inflammatory bowel disease, ulcerative colitis, pancreatitis, and inflammatory peritonitis, asthma.

MAMA (Apopain, CPP32,Diseases in which Barr et al., BiolTechnology, Caspase 3), FLICE disregulated apoptosis12:487-493 (1994) (MchS, plays a Caspase 8), and role in pathology:
other caspases Solid tumors, B cell lymphoma, chronic lymphocytic leukemia, prostate hypertrophy, preneoplastic liver foci, resistance to chemotherapy, stroke, Alzheimer's disease, Parkinson's disease, multiple sclerosis, prion-associated disorders, ataxia telangiectasia, ischemic cardiac damage, chemotherapy-induced myocardial suppression, AIDS, type I diabetes, lupus erythematosus, Sjogren's syndrome, glomeruionephritis, dysentery, inflammatory bowel disease, radiation-and HN induced diarrhea, polycystic kidney disease, anemia or erythropoiesis.

Malarial HemoglobinaseMalaria Rockett, et al., FEB, 259:257-259 (1990) Der p 1 Asthma, house dust Kalsheker, et al., mite Biochem.

allergy Biophys. Research Comm., 221:59-61 (1996) Gingipain K and Adult PeriodontitisWingrove, et al., J. Biol.

S Gingipain R Chem., 267:18902-18907 (1992); DiScipio et al., Immun., 87:660-667 (1996) Cathepsin B, CathepsinOsteoarthritis, Velasco, et al., L, osteoporosis, J. Biol.

Cathepsin S, Cathepsinrheumatoid arthritis,Chem., 269:27136-27142 O and Cathepsin K Alzheimer's disease,(1994); Takeda et cancer al., FEBS

invasion and Metastasis,Letters, 359:78-80 (1995);

Parkinson's disease,Elliott et al., Persp.
in Drug leukemia, lymphoma,Disc. and Des., 6:12-32 hodgkin's disease, (1996) tumors, including those of the bladder, brain, lung, pancreas, prostate, stomach and thyroid Cancer Procoagulant Cancer (including Alessio et al., Eur.
carcinomas J.

of the liver, lung,Haematology, 45:78-8I
breast, kidney, colon, kidney;(1990); Gordon, Seminars osteo-, in chondro-, and liposarcoma;Thrombosis and Hemostasis, neuroblastoma; melanoma;18:424-433 (1992) nonlympocytic leukemia;

lymphocytic leukemia) Calpain I and II Osteoporosis, stroke,Karlsson, et al., CNS Neurobiology injury, Alzheimer'sofAging, 16:901-906 disease (1995);

Additionally, diseasesSquier; et aL, J.
Cell.

involving dysregulatedPhysiol., 159:229-237 apoptosis as listed(1994).
for caspase above.

Calpain p94 Muscular dystrophy Calpain p94 and limb-girdle muscular dystrophy, /COP

Letters 1996.

Hepatitis C Vitvs Hepatitis C Grakoui, et al., Proc. Nat.

Endopeptidase 2 and Acad Sciences, 90:10583-Hepatitis C Virus 10587 (1993) Endopeptidase Picornain 2A and Rhinovirus, polio, Palmenberg, J. Cell.
Picornain enterovirus 3C Proteases infection, common Biochem. 33:191-198 cold, (1987);

aseptic meningitis,Cordingley, et al., polio J.

virology, 5037-5045 (Dec 1989) Hepatitis. A Viral Hepatitis A Krausslich, et al., Protease Annu. Rev.

Biochem., 57:701-754 ( 1988).

Foot and Mouth DiseaseFoot and mouth diseaseRoberts et al., Virology Virus L Protease (Cattle) 213:140-146 (1995) Although the compounds described herein and/or their salts may be administered as the pure chemicals, it is preferable to present the active ingredient as a pharmaceutical composition.
The invention thus further provides the use of a pharmaceutical composition comprising one or more compounds and/or a pharmaceutically acceptable salt thereof, together with one or more pharmaceutically acceptable carriers thereof and, optionally, other therapeutic and or prophylactic ingredients. The carriers) must be 'acceptable' in the sense of being compatible with the other ingredients of the composition and not deleterious to the recipient thereof.
Pharmaceutical compositions include those suitable for oral, topical or parenteral (including intramuscular, subcutaneous and intravenous) administration. The compositions may, where appropriate, be conveniently presented in discrete unit dosage forms and may be prepared by any of the methods well known in the art of pharmacy. Such methods include the step of bringing into association the active compound with liquid carriers, solid matrices, semi-solid carriers,.finely divided solid carriers or combination thereof, and then, if necessary, shaping the product into the desired delivery system.
Pharmaceutical compositions suitable for oral administration may be presented as discrete unit dosage forms such as hard or soft gelatin capsules, capsules, cachets or tablets each containing a predetermined amount of the active ingredient; as a powder or as granules; as a solution, a suspension or as an emulsion. The active ingredient may also be presented as a bolus, electuary or paste. Tablets and capsules for oral administration may contain conventional excipients such as binding agents, fillers, lubricants, disintegrants, or wetting agents. The tablets may be coated according to methods well known in the art., e.g., with enteric coatings.
Oral liquid preparations may be in the form of, for example, aqueous or oily suspension, solutions, emulsions, syrups or elixirs, or may be presented as a dry product for constitution with water or other suitable vehicle before use. Such liquid preparations may contain conventional additives such as suspending agents, emulsifying agents, non-aqueous vehicles (which may include edible oils), or preservative.
The compounds may also be formulated for parenteral administration (e.g., by injection, for example, bolus injection or continuous infusion) and may be presented in unit dose form in ampules, pre-filled syringes, small bolus infusion containers or in multi-dose containers with an added preservative. The compositions may take such forms as suspensions, solutions, emulsions in oily or aqueous vehicles, and may contain formulatory agents such as suspending, stabilizing and/or dispersing agents. Alternatively, the active ingredient may be in powder form, obtained by aseptic isolation of sterile solid or by lyophilization from solution, for constitution with a suitable vehicle, e.g., sterile, pyrogen-free water, before use.
For topical administration to the epidermis, the compounds may be formulated as ointments, creams or lotions, or as the active ingredient of a transdermal patch. Suitable transdermal delivery systems are disclosed, for example, in Fisher et al.
(U.S. Patent No.
4,788,603) or Bawas et al. (tJ.S. Patent No. 4,931,279, 4668,504 and 4,713,224). Ointments and creams may, for example, be formulated with an aqueous or oily base with the addition of suitable thickening and/or gelling agents. Lotions may be formulated with an aqueous or oily base and will in general also contain one or more emulsifying agents, stabilizing agents, dispersing agents, suspending agents, thickening agents, or coloring agents.
The active ingredient can also be delivered via iontophoresis, e.g., as disclosed in U.S.
Patent Nos.
4,140,122, 4,383,529, or4,051,842.
Compositions suitable for topical administration in the mouth include unit dosage forms such as lozenges comprising active ingredient in a flavored base, usually sucrose and acacia or tragacanth; pastilles comprising the active ingredient in an inert base such as gelatin and glycerin or sucrose and acacia; mucoadherent gels, and mouthwashes comprising the active ingredient in a suitable liquid carrier.
When desired, the above-described compositions can be adapted to provide sustained release of the active ingredient employed, e.g., by combination thereof with certain hydrophilic polymer matrices, e.g., comprising natural gels, synthetic polymer gels or mixtures thereof.
The pharmaceutical compositions according to the invention may also contain other adjuvants such as flavorings, coloring, antimicrobial agents, or preservatives.
The compositions may also be administered via inhalation, using a suitable delivery vehicle.
It will be further appreciated that the amount of the compound, or an active salt or derivative thereof, required for use in treatment will vary not only with the particular salt selected but also with the route of administration, the nature of the condition being treated and the age and condition of the patient and will be ultimately at the discretion of the attendant physician or clinician.

In general, however, a suitable dose will be in the range of from about 0.5 to about 100 mg/kg/day, e.g., from about 10 to about 75 mglkg of body weight per day, such as 3 to about 50 mg per kilogram body weight of the recipient per day, preferably in the range of 6 to 90 mg/kg/day, most preferably in the range of 15 to 60 mg/kg/day.
$ The compound is conveniently administered in unit dosage form; for example, containing to 1000 mg; conveniently 10 to 750 mg, most conveniently, 50 to 500 mg of active ingredient per unit dosage form.
Ideally, the active ingredient should be administered to achieve peak plasma concentrations of the active compound of from about 0.5 to about 75 pM, most preferably, about 1 to 50 pM, most preferably, about 2 to about 30 uM. This may be achieved, for example, by the intravenous injection of a 0.05 to 5% solution of the active ingredient, optionally in saline, or orally administered as a bolus containing about 1-100 mg of the active ingredient. Desirable blood levels may be maintained by continuous infusion to provide about 0.01-5.0 mg/kglhr or by intermittent infusions containing about 0.4-15 mg/kg of the active ingredient(s).
The desired dose may conveniently be presented in a single dose or as divided doses administered at appropriate intervals, for example, as two, three, four or more sub-doses per day.
The sub-dose itself may be further divided, e.g., into a number of discrete loosely spaced administrations; such as multiple inhalations from an insufflator or by application of a plurality of drops into the eye.
The inhibitors described herein may be also used for the detection and quantification of the activity of a cysteine protease in a pure sample, mixture or biological fluid or tissue. The activity can be measured with a protease substrate in the absence and presence of a known concentration of the inhibitor. Specific inhibitors can also be used to confirm that the observed activity is due to a particular protease.
The inhibitors described herein may also be used to identify and purify cysteine proteases. The inhibitors can be covalently linked to a solid support, such as an affinity column or beads used in batch methods, and used to purify a protease or enrich a mixture containing the protease. The inhibitor may be linked to the solid support or bead either directly or via a linker of variable length, such that linkage does not interfere with the binding properties (see, e.g., Thornberry, N., Methods in Enz., 244:615-31 ( 1994)) While the invention has been described in connection with specific embodiments thereof, it will be understood that it is capable of further modifications and this application is intended to cover any variations, uses, or adaptations of the invention following, in general, the principles of the invention and including such departures from the present disclosure as come within known or customary practice within the art to which the invention pertains and as may be applied to the essential features hereinbefore set forth, and as follows in the scope of the appended claims.
The following examples are given to illustrate the invention and are not intended to be inclusive in any manner:
Abbreviations used herein are defined as follows:
DMF - dimethylformamide; HBTU - 2-(1H-benzotriazole-1-yl)-1,1,3,3-tetramethyluronium hexafluorophosphate; DIEA - diisopropylethylamine; THF - tetrahydrofiuan;

acetonitrile; EDTA-Naz - ethylenediaminetetraacetic acid disodium salt; Mtr -4-methoxy-2,3,6-trimethylbenzene sulfonyl; Bop-Cl - bis(2-oxo-3-oxazolidinyl)phosphinic chloride; EtOH -ethylalcohol; EtOAc - ethyIacetate; LDA - lithium diisopropylamide; EDCI - 1-(3-dimethylaminopropyl)-3-ethylcarbodiimide hydrochloride; NMM - N-methyl morpholine;
HOBT - 1-hydroxybenzotriazole; TFA - trifluoroacetic acid.
Example I - Synthesis of (~2-~5-(3-methylberuyl)-1,3,4-oxadiazolylJcarbonylJ-2-(S)-methylpropylJ-L phenylalanamide-(3R)-(isobutyl)succinic acid (CM-0019).
The intermediate (benzyloxycarbonyl)-L-valyl-N-[1-(2-[5-(3-methylbenzyl)-1,3,4-oxadiazolyl]hydroxymethyl)-2-(S)-methylpropyl]-L-prolinamide was prepared as follows:
a. 3-(S)-Amino-2-(R,S)-hydroxy-4-methyl pentanoic acid To a solution containing 3-(S)-[(benzyloxycarbonyl)amino]-2-acetoxy-4-methylpentanenitrile (see example 1 of WO 96/16080) (15.2 g, SO.O mmol) in 183 mL of dioxane was added 183 mL of concentrated hydrochloric acid and 7.45 mL of anisole. The reaction mixture was heated to reflux overnight. The hydrolysis reaction was allowed to cool to room temperature and then concentrated in vacuo. The resulting aqueous solution was extracted with ether (2X). The aqueous phase was placed on a Dowex SOXB-100 column (H+
form, preeluted with deionized water to pH = 7). The column was eluted with 2.0 N
ammonium hydroxide and the pure fractions concentrated to afford S.S3 g (7S %) of 3-(S)-amino-2-(R, S)-hydroxy-4-methylpentanoic acid as a pale yellow solid. FAB MS [M+H] m/z;
Calcd: 148, Found: 148.
b. 3-(S)-((Benzyloxycarbonyl)amino]-2-(R,S)-hydroxy-4-methyl pentanoic acid.
To a solution under an atmosphere of nitrogen containing 1.0 g (6.8 mmol) of 3-(S)-amino-2-(R,S)-hydroxy-4-methylpentanoic acid in 9.S mL of 1 N NaOH and 10 mL
of dioxane was added i .43 g (8.4 mmol) of benzyl chloroformate. The pH was maintained above pH 8 with 1 N NaOH as needed. The reaction mixture was allowed to stir at room temperature overnight.
The reaction was diluted with water and washed with ether. The aqueous layer was acidified with 1 N HCl to pH = 2 and extracted with ether (2X). The combined organic layers were dried over magnesium sulfate, filtered and evaporated in vacuo to afford 1.75 g (92%) of 3-(S)-[(benzyloxycarbonyl)aminoJ-2-(R,S)-hydroxy-4-methylpentanoic acid as a light yellow viscous oil. FAB MS [M+H) m/z; Calcd: 282, Found: 282.
c. 3-(S)-~(Benzyloxylcarbonyl)amino]-2-(R,S)-acetoxy-4-methyl pentanoic acid.
To a solution of 3-(S)-[benzyloxycarbonyl)amino]-2-(R,S)-hydroxy-4-methylpentanoic acid (1.70 g, 6.04 mmol) and pyridine (4.9 mL) was added acetic anhydride (S.7 mL, 6.17 g, 60.4 mmol) dropwise at room temperature. The reaction was allowed to stir overnight and was diluted with ethyl acetate and washed with water (2X). The organic layer was dried over magnesium sulfate, filtered and evaporated in vacuo to give a thick oil. The residue was purified by column chromatography on silica gel with 1S% methanol/dichloromethane to afford 1.56 g (80%) of 3-2S (S)-[(benzyloxycarbonyl)amino)-2-(R, S)-acetoxy-4-mcthyl pentanoic acid as a light yellow viscous oil. FAB MS [M+H] m/z; Calcd: 324, Found: 324.
d. 1-~(3-Methylpherrylacetyl)-2-(2-(R,S)-acetoxy)-3-(S)-~(benzyloxycarbonyl)aminoJ-4-methylpentanoylJ hydrazine.
To a solution containing 3-(S)-[(benzyloxycarbonyl)amino]-2-(R,S)-acetoxy-4-WO 99!54317 PCT/US99/08501 methylpentanoic acid (2.3 g, 7.11 mmol) in 40 mL of DMF under a nitrogen atmosphere at O°C
was added 1.31 g (9.69 mmol) of HOBT and 1.36 g (7.09 mmol) of EDCI. After stirring for 30 minutes, 1.20 g (7.3 I mmoi) of 3-methylphenyl acetic hydrazide [prepared analogously to the monoacid hydrazides cited by Rabins et. al. (J. Org. Chem., 30:2486 (1965))]
and 1.0 mL (9.10 mmol) of NMM were added. The reaction was allowed to warm to room temperature and stir overnight. The reaction was diluted with ethyl acetate and washed with 5%
potassium hydrogen sulfate, saturated sodium bicarbonate, brine and water. The organic phase was dried over magnesium sulfate, filtered and evaporated under reduced pressure. The residue was purified by column chromotography on silica gel with 10% methanol/dichloromethane to afford 2.31 g {89.0%) of the title compound as a white solid. FAB MS [M+H] m/z; Calcd: 470, Found: 470.
e. I - j2- j5-(3-Methyl benzyl)-I , 3, 4-oxodiazolylJ-I -acetoxy-2-(S)-(berrryloxycarborryl)arninoJ-3-methylbutane.
A solution containing 2.31 g (4.92 mmol) of 1-[(3-methylphenylacetyl)-2-(2-(R, S)-acetoxy)-3-(S)-[(benzyloxycarbonyl)amino]-4-methylpentanoyl]hydrazine in 25 mL
of pyridine and 1.88 g (9.86 mmol) of toluene sulfonyl chloride was heated at reflux under a nitrogen atmosphere for 72 hours. The solvent was removed under reduced pressure and the residue dissolved in ethyl acetate and washed with water. The organic phase was dried over magnesium sulfate, filtered and evaporated under reduced pressure. The residue was purified by column chromatography on silica gel with 5% ethyl acetate/hexane to afford 1.41 g (63.5%) of the title compound. FAB MS (M+H] m/z; Calcd: 452, Found: 452.
f. I - j2- j5-(3-Methylbenzyl)-1, 3, 4-oxadiazolyl)J-2-(S)-(benzyl oxycarborryl)am inoJ-3-methylbutan-I-ol.
A solution containing 1.80 g (3.99 mmol) of 1-[2-[5-(3-methylbenzyl)-1,3,4-oxadiazolyl)-1-1-acetoxy-2-(S)-(benzyloxycarbony!)amino]-3-methylbutane and 0.72 g (5.21 mmol) of potassium carbonate in 30 mL of methanol and 8 mL of water was allowed to stir at room temperature for 30 minutes. The solvent was removed under reduced pressure and the residue dissolved in ethyl acetate and washed with water. The organic phase was dried over magnesium sulfate, filtered and evaporated under reduced pressure. The residue was purified by column chromatography on silica gel with 60% ethyl acetate/hexane to afford 1.46 (89.3%) of the title compound. FAB MS [M+H] m/z; Calcd: 410, Found: 410.
g. l-~2-(5-(3-Methylbenzyl)-1,3,4-oxadiazolylJ-2-(S) Amino-3-methylbutan-I-of hydrochloride.
To a solution containing 1.31 g (3.20 mmol) of 1-[2-[5-(3-methylbenzyl)-1,3,4-S oxadiazolyl]-2-(S)-(benzyloxycarbonyl)amino]-3-methylbutan-1-of in 25 mL of trifluoroacetic acid under a nitrogen atmosphere at O °C was added 0.43 mL (3.94 mmol) of thioarusole. The reaction was allowed to warm to room temperature overnight. The solvent was removed under reduced pressure and the residue dissolved in ether and cooled to -78°C
under a nitrogen atmosphere. To this solution was added 3 mL (3 mmol) of 1 N hydrochloric acid in ether. The resulting white solid was allowed to settle and the ether decanted. Additional ether was added and decanted (3X). The solid was dried under vacuum to afford 0.92 g (92.2%) of the title compound. FAB MS [M+HJ m/z; Calcd: 276, Found: 276.
(4S)-4-Benzyl-3-(4 =(methyl)pentanoylJ-2-oxazolidinone a. 4-Methylvaleric acid (6.56 g, 55.6 mmol) was dissolved in dry CHZCIZ(40 ml) under N, and chilled to 4°C. Oxalyl chloride (5.4 mL, 63.5 mmol) was added;
followed by 4 drops of dry DMF. Rapid COZ evolution occured. The reaction mixture was allowed to warm to ambient temperature over 2 h; no more COZ evolution was apparent. Solvents were stripped by rotary evaporation and the acid chloride was distilled in vacuo. 'H-NMR (300 MHz, CDCl3) 8 0.88-0.93 (m, 6H), 1.59-1.64 (m, 3H), 2.90 (t, 2H, J= 7.5 Hz).
b. (S)-(-)-4-benzyl-2-oxazolidinone (8.93 g, 50.4 mmol) was dissolved in dry THF under Nz and chilled to -78°C. nButyl lithium (1.6 M in hexane, 32 mL, 50.4 mmol) was added dropwise to maintain temperature < -70°C. The mixture was stirred 25 min. at -78 °C, then a solution of the acid chloride prepared above in dry THF (30 mL) was added dropwise to maintain temperature <-65°C. The reaction mixture was stirred overnight and allowed to warm to 15°C.
The reaction was quenched by careful addition of saturated NH,CI (70 mL). THF
was removed under reduced pressure and the resultant aqueous slunry was extracted with EtOAc (100 mL).
The organic layer was washed with 0.5 N NaOH, HBO, brine. The organic layer was dried over MgS04, filtered and evaporated in vacuo to return 12.7 g of crude yellow oil.
The crude material WO 99/54317 PC'T/US99/08501 was purified by silica gel chromatography (10% EtOAc/hexane) and dried in vacuo to return 9.0 g (69% yield) of pale yellow oil. C-18 HPLC RT = 16.5 min., 96% pure at 21 S
nm (10-100%
solv. B/25 min; solvent A= 0.1% (v/v)TFA/H20; solvent B = 0.1%
TFA/acetonitrile; FAB-MS
m!z 276(M+H) ;'H-NMR (300 MHz, CDCI,) x0.94 (d, 6H, J=6.3 Hz, e-[(CH3)Z]), 1.53-1.72 (m, 3H, [i CH2,g CH), 2.76 (dd, 1H, J=13.3, 9.6 Hz, oxazolidinone 5-CHI), 2.90-2.97 (m, 2H), 3.29 {dd, 1H, J=13.2, 3.3 Hz, oxazolidinone SC~IH), 4.15-4.20 (m, 2H), 4.64-4.70 (m, 1H, oxazolidinone 4-CH), 7.17-7.39 (m, SH, Ph-H).
c. (4S)-4-Ben.,ryl-3-(2'R)-2 =~((tert-butoxycarbonyl)methylJ-4 =(methyl)pentanoylJ-2-oxazolidinone.
Diisopropylamine (5.05 mL, 36 mmol) was diluted with dry THF (20 mL) and chilled to -20°C under NZ. n-Butyl lithium (1.6 M in hexane, 23 mL, 36 mmol) was added dropwise to maintain the temperature <-10°C. The temperature was increased to 4°C and stir ed 30 minutes to generate LDA. The flask was chilled to -78°C and (4S)-4-Benzyl-3-[4'-(methyl)pentanoyl]-2-oxazolidinone in dry THF {1S mL) was added dropwise to maintain the temperature < -70°C.
The reaction was stirred 30 minutes at -78°C then t-butylbromoacetate (4.9 mL, 33 mmol) in dry THF was added dropwise to maintain the temperature <-65°C. The mixture was stirred and allowed to warm to -10°C overnight. After 15 hours, the reaction was quenched by careful addition of water followed by evaporation of the THF. Water (100 mL) was added to the slurry.
and the crude mixtrure was extracted with EtOAc (100 mL). The organic layer was washed with water and brine; then dried over MgSO,, filtered and dried in vacuo to leave 13.3 g crude yellow oil. Silica gel chromatography in 15% EtOAclhexane returned 7.84 g (61% yield ) of a white solid product.
C-18 HPLC RT = 19.5 min., 99% pure at 215 nm (10-100% solv. B/25 min; solvent A= 0.1%
(v/v)TFA/H~O; solvent B = 0.1% TFA/acetonitrile; FAB-MS mlz 390 (M+H)', 334 (M-tBu+H)'.
'H-NMR (300 MHz, CDCh) 80.92 (d, 3H, J=6.0 Hz), 0.94 (d, 3H, J=5.8 Hz), 1.28-1.40 (m, 1H, C~IvIe2),1.43 (s, 9H3), 2.49 (dd, 1H, J=16.7, 4.6 Hz), 2.72 (dd, 1H, J=10.3, 1.1 Hz), COzC
(CH3)3), 2.76 (dd, 1H, J=10.3, 2.2 Hz, Ph-CHI, 3.35 (dd, 1H, J=13.5, 3.1 Hz), 4.15-4.18 (m, 2H), 4.21 -4.26 (m, 1H), 4.52-4.61 (m, 1H), 7.27-7.34 (m, SH, Ph-H).

d. (2R)-2-((tert-Butoxycarborryl)methylJ-4-(methyl)pentanoic acid (4S)-4-Benzyl-3-(2'R)-2'-[[(tert-butoxycarbonyl)methyl]-4'-(methyl)pentanoyl]-oxazolidinone (5.89, 15.1 mmol) was dissolved in dry THF(100 mL) and water (25 mL) was added. The mixture was chilled to 4°C under NZ. HZOZ (7.6 mL) was added followed by S dropwise addition of LiOH (0.76 g, 18.2 mmol) in H20 (20 mL) over 20 minutes. The mixture was stirred for 1 hour and allowed to warm to ambient temperature. The mixture was again chilled in an ice bath and quenched by addition of Na2S03 (3.1 g) in water (20 mL). THF was removed by rotovap, the remaining aqueous layer was washed with EtOAc (4x70 mL), then acidified to approx. pH 2 with conc. HCl after layering with fresh EtOAc. The mixture was immediately extracted with EtOAc (3x80mL). The combined EtOAc extracts were dried over MgS04, filtered, and evaporated to return 3.29 g clear oil (95% crude yield) which showed no traces of starting material by HPLC. This material was used without further purification.
'H-NMR (300 MHz, CDC13) 80.90 (d, 3H, J=6.4 Hz, CH3), 0.94 (d, 3H, J=6.5 Hz, CH3), 1.20-1.48 (m, 1H, CHMez), 1.44 (s, 9H, C(CH,),), 1.50-1.72 (m, 2H), 2.37(dd, 1H, J=16.4, 2.4 Hz), 2.59 (dd, 1 H, J=16.4, 2.6 Hz), 2.80-2.95 (m, 1 H).
e. Tert-butyl(3R)-3-(isobutyl)succinyl-L phenylalartyl methyl ester.
To a solution of tent-butyl-(3R)-3-(isobutyl)succinate (10.82 g, 47.0 mmols), in 90 ml of dry DMF was added HBTU (17.45 g, 46.0 mmols), followed by DIEA (18.43 g, 142.6 mmols).
After stirring for 10 min, L-phenylalanine methyl ester hydrochloride (10.0 g, 46.36 mmols) was added. This was allowed to stir at room temperature overnight. The solvent was removed under reduced pressure and the residue dissolved in 200 ml ethyl acetate. This solution was washed with water, 1 M HCI (2x), saturated NaHC03 (2x), brine, and the organics were dried with anhydrous MgSO,,. The mixture was filtered and the solvent removed under reduced pressure.
The residue crystallized to an off white solid upon sitting overnight, giving 13.3 g (74%) of tert-butyl(3R)-3-(isobutyl)succinyl-L-phenylalanyl methyl ester. C-18 HPLC RT =16.9 min., 98%
pure at 215 nm (10 to 100% solvent B/25 min; solvent A = 0.1% TFA/HZO; solvent B = 0.1%
TFA/acetonitrile).
FAB-mass spectrum: m/z (M+H)' = 392; Theory = 392.

'H NMR (CDCl3) 8 [0.85 (d, J= 7.5 hz); 0.88 (d, J= 7.5 hz); 6H]; [1.10-1.23 (m, 1H)];
[1.44 (s, 9H)]; [1.45-1.65 (m, 2H)]; [2.22-2.32 (m, 1H)]; [2.50-2.66 (m, 2H)];
[3.10 (d, J= 6 Hz}
2H]; [3.69 (s,3H)]; [4.82-4.92 (m, 1H)]; [6.19 (d, J= 9 hz), lH]; [7.13-7.33 (m, 5H)].
f. Tert-butyl(3R)-3-(isobutyl)succinyl-L phenylalanine.
A solution of tert-butyl(3R)-3-(isobutyl)succinyl-phenylalanyl methyl ester (2.0 g, 5.10 mmols} in 5 ml methanol was cooled to 4°C in an ice bath. To this solution was added 4 ml of an aqueous solution of lithium hydroxide (333 mg, 7.94 mmols.), and this solution was stirred and allowed to warm to room temperature overnight. The solution was concentrated to an oil under reduced pressure. The residue was dissolved in 100 ml ethyl acetate, washed with 10%
citric acid, water, and dried with anhydrous MgSO,. The mixture was 'filtered and the solvent was removed under reduced pressure, vacuum dried overnight to give 1.8 g (95%}of tert-butyl(3R)-3-(isobutyl)succinyl-L-phenylalanine as a light yellow oil. C-18 HPLC RT = 14.7 min., 95% pure at 254 nm (10 to 100% solvent B/25 min; solvent A = 0.1%
TFA/HZO; solvent B
1 S = 0.1% TFA/acetonitrile).
FAB mass spectrum: M+H = 378; theory = 378.
'H NMR (CDC13) 8 [0.83 (d,J = 6.0 hz); 0.85 (d, J = 6.0 hz); 6H]; [1.10-1.25 (m, 1H)];
[1.44 (s, 9H)]; [1.45-1.65 (m, 2H)]; [2.24-2.35 (m, 1H)]; [2.48-2.58 (m, 2H)];
[3.07-3.27 (m,2H)]; [4.79-4.93 (m, 1H)]; [6.36 (d, J = 9 Hz), 1H]; [7.20-7.41 (m, 5H)].
zo g. Tert-butyl(3R)-3-(isobutyl)succirryl-~(2-(5-(3-methylbenryl)-1,3,4-oxadiazolylJ-(R,S)-hydroxymethylJ-2-(S)-methylpropylJ-L phenylalaninamide.
To a solution of tert-butyl(3R)-3-(isobutyl)succinyl-phenylalanine (1.8 g, 4.80 mmols) in 40 ml'DMF was added HOST (676 mg, 5.0 mmols). This was cooled in an ice bath to 4°C.
25 EDCI (921 mg, 4.80 mmols) was then added. After stirring for 30 minutes, a solution of [2-(5-(3-methylbenzyi)-1,3,4-oxadiazolyl]-2-(S)-amino-3-methylbutan-1-(R,S)-of hydrochloride(1.50 g, 4.24 mmols) in 20 ml. DMF was added dropwise, followed by N-methyl morpholine (0.77 g, 7.66 mmols) and the reaction allowed to stir and warm to room temperature overnight. Most of the solvent was removed under reduced pressure and the mixture was diluted with ethyl acetate.

It was then washed with saturated NaHC03, 5% KHSO,, brine, and the organics dried with anhydrous MgSO,. The mixture was filtered and the solvent removed under reduced pressure.
The residue was purified by column chromatography (silica gel, ethyl acetate:hexane 50:50 to 65:35) to give 1.30 g, 43% of tert-butyl(3R)-3-(isobutyl)succinyl-[[2-[5-(3-methylbenzyl)-1,3,4-oxidiazolyl]-(R,S)-hydroxymethyl]-2-(S)-methylpropylJ-L-phenylalaninamide as an off white foamy solid. C-18 HPLC RT = 18.3, 18.7 min. diastereomers, 90% pure at 215 nm (10 to 100%
solvent BI25 min; solvent A = 0.1 % TFA/HzO; solvent B = 0.1 %
TFA/acetonitrile).
FAB mass spectrum: m/z (M+H)' = 635; theory = 635.
h. tert-Butyl(3R)-3-(isobutyl)succinyl-~~2-(S-(3-methylbenzyl)-1,3,4-oxadiazolylJcarbonylJ-2-(S)-methylpropylJ-L phenylalaninamide.
To a stirred mixture ofN-chlorosuccinimide (1.07g, 8.0 mmols) in 25 ml dry toluene at 4 ° C was added 0.84 ml ( 11.45 mmols) dimethyl sulfide (DMS) under a nitrogen atmosphere. A
white precipitate formed after the addition of DMS. After 30 minutes, the resulting suspension was cooled to -25 °C using a carbon tetrachloride and dry ice bath. A
solution of tert-butyl(3R)-3-(isobutyl)succinyl-[[2-[5-(3-methylbenzyl)-1,3,4-oxadiazolyl]-(R,S)-hydroxymethyl]-2-(S)-methylpropylJ-L-phenylalaninamide (1.25g, 1.97 mmols) in 30 ml dry toluene was added dropwise. The resulting mixture was stirred for 1.5 h at -25°C and 1.19 ml (8.5 mmols) of triethylamine was added. After 15 minutes, the cold bath was removed, and the reaction monitored by TLC; silica gel; ethyl acetate:hexane (30:70). After 1 h, the mixture was diluted with 500 ml ethyl acetate and washed with saturated NaHC03 brine and the organics dried with anhydrous MgSO,,. The mixture was filtered and the solvent removed under reduced pressure.
The residue was purified by column chromatography (silica gel, methanol:chloroform, 0.5:99.5 to 2.5:97.5) to give tert-butyl(3R)-3-(isobutyl)succinyl-[[2-[5-(3-methylbenzyl)-1,3,4-oxadiazolyl]carbonylJ-2-(S)-methylpropylJ-L-phenylalaninamide as an off white foamy solid;
1.0 g, (80.2%). C-18 HPLC RT = 20.2, 20.7 min. diastereoisomers, 90% pure at 215 nm (10 to 100% solvent B/25 min; solvent A = 0.1% TFA/H20; solvent B = 0.1%
TFAlacetonitrile).
FAB mass-spectrum: m/z (M+H); = 633; theory = 633.

i. jj2-j5-(3-methylbenzyl)-1,3,4-oxadiazolylJcarbonylJ-2-(S)-methylpropylJ-L-phenylalaninamide-(3R)-(isobutyl)succinic acid.
To a solution of tert-butyl(3R)-3-(isobutyl)succinyl-[2-[S-(3-methylbenryl)-1,3,4-oxadiazolylJcarbonylJ-2-(S)-methylpropylJ-L-phenylalaninamide (1.0 g, 1.58 mmol) in 25 ml dichloromethane (DCM) cooled to 4°C in an ice bath, was added 25 ml trifluoroacetic acid (TFA). This was stirred for 1 h. The solvent and TFA are removed under reduced pressure, followed by coevaporation with DCM (3x). The material was purified via gradient RP-HPLC
CH,CN:H~O (25:75 to 100:0 in 60 minutes) to give 292 mg (32%, 0.51 mmols) of which 52 mg was pure as a white solid after lyophilization. C-18 HPLC RT = 15.8 min., 95%
pure at 215 nm ( 10 to 100% solvent B/25 min; solvent A = 0.1 % TFA/HZO; solvent B = 0.1 %
TFA/acetonitrile).
FAB Mass spectrum: m/z (M+H)' = 577; theory = 577. 'H-NMR(400 MHz, CDCI;)8 0.76 (d, 3H, J=6.8 Hz), 0.85 (d, 3H, J=6.4 Hz), 0.87 (d, 3H, J=6.4 Hz), 0.93 (d, 3H, J=6.8 Hz), 1.25-1.32 (m, 1H), 1.48-1.61 (m, 2H), 2.28-2.36 (m, 2H), 2.35 (s, 3H), 2.44-2.49 (m, 1H), 2.6I-2.69 (m, 2H), 2.95 (dd, 1H, J=13.6, 8.4 Hz), 3.09 (dd, 1H, J=16.6,6.4 Hz),4.24 (s, 2H), 4.67 (dt, 1H, J=8.0, 6.8 Hz), 5 .19 (dd, 1 H, J=8.4, 6.0 Hz), 6.52 (br. d, 1 H, J=8.4 Hz), 6.81 (br. d, l H, J=7.6 Hz), 6.94-6.99 (m, 1H), 7.10-7.19 (m, 7H). '3C-NMR(100 MHz, CDC13) a 17.26, 19.54, 21.33, 22.13, 22.71, 25.75, 30.84, 31.82, 36.74, 38.16, 40.54, 41.29, 55.16, 61.55, 126.1, 126.8, 128.6, 128.8, 129.0, 129.1, 129.7, 132.5, 136.2, 139.0, 160.2, 167.9, 171.6, 175.0, 175.7, 184.4.
Example II -Acetyl-L-leucyl-N jl-j2-j(5 phenyl)-1,3,4-oxadiazolyl]carbonyl]-4-(guanidino)-butyl]-L-leucylJamidE (CQ-0002).
2-Pherryl-1,3,4-oxadiazole intermediate Benzoyl hydrazide (200 mg) freshly crystallized from chloroform was suspended in 5 mL
of triethyl orthoformate and heated at reflux under nitrogen in a 160 °C oil bath for 3 hours. The mixture was cooled to room temperature, chilled in ice, and treated with 50 mL
water and 10 mL
10% KHS04 solution. The mixture was stirred approximately 2 minutes then 50 mL
of EtOAc was added and stirring continued for 10 minutes. The organic layer was separated and the aqueous layer was extracted three times with ethyl acetate. All ethyl acetate layers were combined and were washed with 10% sodium bicarbonate solution and saturated sodium chloride solution. Drying over sodium sulfate, rotary evaporation and further drying under high vacuum provided 204 mg of an analytically pure oil which crystallizes upon standing.
Commercially available benzoylhydrazide (Aldrich) in this reaction may be used, but the resulting product often contains a minor impurity which can be removed following the cyclization, by flash chromatography on silica gel eluting with 0 - 10% acetone in hexane.
'H-NMR-CDCI3 7.49-7.62 (m, 3H), 8.12 (d, J=6, 2H), 8.49 (s, 1H).
A. Acetyl-L-leucyl-L-leucyl-arginine(Mtr) (N methyl)-(N Methoxy)-amide: Acetyl-Leu-Leu-OH (133 mg) and arginine (Mtr) -N-methyl-N-methoxy amide (200 mg) were dissolved in 10 mL of DMF and were treated with 243 uL of DIEA and 212 mg of HBTU. The reaction stirred at room temperature for 1 S hours and was worked up according to method A. Drying over Na,SO,, rotary evaporation of the solvent and flash chromatography on silica gel (50%
acetone in hexane) provided 270 mg of the title compound as a foam.
B. Acetyl-L-leucyl-N jl-j2-j(S phenyl)-1,3,4-oxadiazolylJcarbonylJ-4-j(4-methoxy-2,3,6-trimethyl-benzenesulphonyl)-guanidinoJ-butylJ-L-leucyl amide: 2-phenyl-1,3,4-oxadiazole (194 mg) in 2 mL of dry THF was chilled to -78° C. n-Butyllithium (1.46 mmole) was added as a 2.5 M solution in hexanes. The reaction stirred 20 minutes at -?8°C
and was then placed in a 0°C cooling bath. Acetyl-Leu-Leu-Arg-(Mtr)-N-(CH3)-OCH, was then added in 2 mL of dry THF. The reaction was placed in a room temperature water bath and stirred 1 hour, then the solution was chilled to 0 ° C, and 20 mL of saturated ammonium chloride solution was added under nitrogen with rapid stirring. After the several minutes of vigourous stirring the solution was extracted with EtOAc. The ethyl acetate solution was washed with saturated sodium chloride solution, dried over sodium sulfate and concentrated to a pale brown oil by rotary evaporation.
C. Acetyl-L-leucyl-N jl-j2-j(S pherryl)-1,3,4-oxadiazolylJcarbo~rylJ-4-(guanidi»o)-butylJ-L-leucyl amide: One half of the crude product from step B was dissolved in a pre-formed solution of 2 mL of TFA and 100 uL thioanisole. The reaction stirred under nitrogen for 4 hours.
The solvent was removed in vacuo, and the product was precipitated with dry ether. The precipitate was taken up in methanol and concentrated in vacuo, the residue was triturated with WO 99/54317 PCT/US99/0$501 dry ether, and dried in vacuo to provide 22 mg of the title compound as a colorless powder.
Samples for biological testing were obtained by reverse phase C 18 chromatography (5-80%
CH3CN, 0.1 % TFA, over 40 minutes). MS m/z (M+H)' 571 (CQ-0002).
S Example III -Synthesis ofAcetyl-L-leucyl-N jl-j3-j5-methyl)-1,2,4-oxadiazolylJcarbonylJ-ethyl-L-leucyl amide (CQ-0004) A. N'-benryloxycarbonyl-L-alanine (N methyl-N methoxy)amide: Cbz-L-Alanine (1.0 g) was dissolved in 10 mL dry DMF with 1.55 mI, of DIEA. HBTU (1.78 g) was added and the reaction Stirred 30 minutes. Dimethyl hydroxyl amine hydrochloride (0.87 g) was added followed by 1.55 mL additional DIEA. The reaction stirred approximately 15 hours at room temperature. Work up according to general method A, drying over anhydrous sodium sulfate, rotary evaporation, and drying under high vacuum produced 0.96 g of a colorless solid.
B. N'-benzyloxycarbonyl-L-alaninal: A solution of 6 mL of 1 M lithium aluminum hydride in THF was chilled under nitrogen to 0°C and a solution of compound A (0.68 g ) in 4 mL DMF was added dropwise. After stirring 15 minutes at 0°C the reaction was carefully quenched with 20 mL of EtOAc and 10 mL of 10% KHSO, solution. The organic layer was washed with 1 N HCl and 10% NaHC03 solution. Drying over sodium sulfate, removal of the solvent by rotary evaporation, and drying under high vacuum provided 0.38 g of a colorless oil.
C. 2-(R,S)-3-(S)-j(benzyloxycarbonyl)amino)-1-hydroxy-butanenitrile: Compound B
(1.2 g) triethylamine (0.532 mL) and acetone cyanohydrin (1.56 mL) were dissovled in 10 mL
of dry CHZCIz and stirred at room temperature for approximately 1 S hours. The solvent was removed in vacuo and the residue was taken up in EtzO and washed with saturated sodium chloride solution. Drying over anhydrous sodium sulfate, rotary evaporation, and pumping under high vacuum provided 1.3 g of the cyanohydrin.
D. 2-(R,S)-3-(S)-j(benryloxycarborryl)amino)-1-acetoxy-butanenitrile: Compound C
(1.3 g) was dissolved in 2 mL of dry pyridine and was treated with 3.17 mL of acetic anhydride.
The reaction stirred at room temperature for 3 hours and was then diluted with ethyl acetate and washed with water. Drying of sodium sulfate, rotary evaporation, and pumping under high vacuum provided 1.34 g of the title compound as an oil.

E. I-(R,S)-2-(S)-1-j(N hydroxy)carboximideamidoJ-I-acetoxy-2-j(benryloxycarbonyl)-amino) propane: Compound D (1.34 g) was dissolved in 21 mL of EtOH and 4.2 mL
of water and treated with hydroxylamine hydrochloride (0.422 g) and sodium acetate (0.991 g) and heated at 40 C for 3 hours. The solvent was removed in vacuo and the residue was suspended in EtOAc S and washed with water. Drying over sodium sulfate and evaporation of the solvent provided 1.1 g of crude rizaterial which was used without further purification.
F. 1-(R, S)-2-(S)-1- j3- j5-(methyl)-I , 2, 4-oxadiazvlylJ-I -acetoxy-2(benryl oxycarbonyl)-amino)) propane: Compound E (0.45 g) was suspended in 5 mL toluene and treated with 185 uL of acetic anhydride. The reaction was refluxed for approximately 15 hours, after which the solvent was removed by rotary evaporation and purified by flash chromatography on silica gel eluting with 1:1 hexane:EtOAc to provide 0.36 g of title compound.
G. I -(R,S)-2-(S)-I -j3- j5-(methyl))-l, l, 4-oxadiazolylJ-2-j(benzyloxycarbonyl)-aminoJ-propan-I-ol: Acetate F (180 mg) was dissolved in 3 mL of MeOH and treated with a solution of 90 mg of KZCO~ in 1 mL of water. After approximately 20 minutes the reaction mixture was 1 S diluted with EtOAc and washed with water. Drying over MgSO~, rotary evaporation and drying under high vacuum provided 0.160 g of the title compound.
H. 1-(R,S)-2-(S)-I-j3-j5-(methyl)-1,2,4-oxadiazolylJ-2-amino) propan-l-of TFA
salt:
Compound G was taken in 2 mL of trifluoroacetic acid and chilled to 0°C. Thioanisole (100 uL) was added and the reaction was allowed to warm to room temperature and stirred approximately 15 additional hours. The solvent was removed in vacuo and traces of remaining TFA were removed by rotary evaporation from dichloromethane and methanol. The crude product was partially purified by elution through a pre-packed C18 mini-column (Waters Sep-Pak) with acetonitrile in water. Lyophilization of appropriate fractions provided the title compound 0.14 g, which was used without further purification.
1. 1-(R,S)-2-(S)-(Benzyloxycarbonyl)-L-leucyl-N jl-j(3-j5-(methyl)-1,2,4-oxadiazolylJ-hydroxymethylJ-ethyl J-L-leucine amide: Compound H (0.14 g) and Acetyl-Leu-Leu-OH were dissolved in DMF (3 mL) and were treated with DIEA (90 uL) and HBTU (234 mg).
The reaction was allowed to stir approximately 1 S hours at room temperature. The reaction mixture was diluted with EtOAc and washed with water. The water wash was extracted with dichloromethane. All organic layers were combined and concentrated in vacuo.
The residue was purified by preparative C 18 reverse phase chromatography (5-60% CH3CN, 0.1 %
TFA) to provide 0.110 g of the title compound upon lyophilization.
J. Acetyl-L-leucyl-N ~1-~3-~5-methyl-1,2,4-oxadiazolylJcarbonylJ-ethylJ-L-leucyl amide:
N-chlorosuccinimide (75.4 mg was suspended in dry toluene and chilled to 0°C. Dimethyl sulfide (60 uL) was added and the suspension stirred 30 minutes at 0°C
and was then chilled to -25°C. Compound I ( 60 mg) was added in 2 mL dichloromethane and the reaction stirred 2.5 hours at -25°C. Triethyl amine (84 uL) was added and the reaction warmed to room temperature. After stirring 1 hour the reaction mixture was diluted with EtOAc and was washed with water. Drying over anhydrous sodium sulfate and removal of the solvent by rotary evaporation provided 60 mg of crude product. Flash chromatography on silica gel provided 30 mg of the title compound as a colorless solid. MS 424. (M+H).
1 H-NMR a 0.89 -0.94 (m, 12 H), 1.50 (d, J=9.6, 3H), 1.53-1.69 (m, 6H), 2.01 {s, 3H), 2.70 (s, 3H), 4.50-4.52 (m, 2H), 5.34-5.39 (m, 1H) 6.23 (d, J=11, 1H), 6.81 (d, J=10.9, lI~, 7.07 (d, J=8.8, 1 H). 13C-NMR a 12.4 , 17.6, 22.1, 22.2, 22.8 (2 carbons), 23.1, 24.7, 24.8, 40.8, 41.1, 52.7, 164.1, 170.3, 171.3, 172.3, 178.3, 190.
Example IV -Acetyl-L-leucyl-N ~l-~3-~S-methyl-1,2,4-oxadiazolylJcarbonylJ-4-(guanidino)-butylJ-L-leucyl amide (CQ-0007) A. N'-t-butoxycarbonyl-L Arg(Mtr)-(N methyl-N methoxy)amide: Boc-L-Arg(Mtr)-OH
5.00 g (10.3 mmole) was suspended in dry DMF (10 mL),followed by N,O dimethyl hydroxylamine hydrochloride (1.25 g) and DIEA (5.4 mL). HBTU (4.28 g) was added and the reaction stirred approximately 15 hours at room temperature. The reaction was worked up according to general method A, and the EtOAc solution was dried over Na2S0, and concentrated to 5.23 g of a colorless foam.
B. N'-t-butoxycarborryl-L-(Mtr)-argininal: Compound A (2 .00 g) was dissolved in 20 mL of dry THF and chilled to 0°C. To this solution was added 4.72 mL of a 1 M solution of LiAIH, in THF, dropwise over 30 minutes at 0°C. The reaction was quenched at 0°C by the slow addition of 50 mL EtOAc, followed~by 15 mL of 10% KHS04 solution. The mixture was partitioned between 100 mL EtOAc and 50 mh 1 N HCl solution. The organic layer was washed with 1 N HCl solution and saturated sodium chloride solution. The mixture was dried over anhydrous sodium sulfate and concentrated by rotary evaporation . Drying under high vacuum provided 1.74 g of a white solid.
C. 2-(R,S)-3-(S)-~(t-butoxycarbonyl)amino)-6-((4-methoxy-2, 3, 6-trimethyl-benze»esulphonyl)-guanidinoJ-2-hydroxy-hexanenitrile: Compound B (1.70 g) was dissolved in 25 mL of methanol and was treated with 0.941 g of potassium cyanide. The reaction was allowed to stir at room temperature for approximately 15 hours. The reaction mixture was then partitioned between 150 mL EtOAc and 25 mL 1 N HCI. The organic layer was washed with 1 N
HCl and dried over anhydrous sodium sulfate solution. Rotary evaporation and further drying under high vacuum provided 1.62 g of the title compound.
D. 2-(R,S)-3-(S)-((t-butoxycarbonyl)amino)-6-~(4=methoxy-2, 3, 6- trimethyl-benzenesulphonyl)-guanidinoJ-2-acetoxy-hexanenitrile: Compound C (1.62 g) was dissolved in 10 mL of dry pyridine and treated dropwise with 0.62 mL of acetic anhydride.
The reaction was allowed to stir at room temperature for 3 hours. The solution was diluted with 100 mL EtOAc and washed three times with equal volumes of I N HCl after drying over anhydrous sodium sulfate the solution was concentrated by rotary evaporation to an oil, and purified by flash chromatography on silica gel (50-75% EtOAc in hexanes, step gradient) to provide 0.79 g of the title compound and 0.64 g of mixed fractions containing traces of compound B.
E. 1-(R,S)-2-(S)-1-((N hydroxy)carboximideamidoJ-1-acetoxy-2-~(t-butoxycarbonyl)-aminoJ-S-((4-methoxy-2,3,6-trimethyl-benzenesulphonyl)-guanidinoJ pentane:
Compound D
(0.79 g ) was dissolved in 45 cnL of EtOAc and 3.9 mL of water and was treated with 0.174 g of sodium acetate and 0.129 g of hydroxylamine hydrochloride. In an analogous fashion the mixed fractions containing compound D (0.64 g) were dissolved in 36.5 mL ethanol and 3.2 mL of water and were treated with 0.141 g of sodium acetate and 0.105 g of hydroxylamine hydrochloride. The reactions were heated at 45 °C for 4 hours with stirring. HPLC analysis showed very similar profiles for both reactions. The reactions were diluted with EtOAc, washed with water and saturated sodium chloride solution and were then dried over anhydrous sodium sulfate and concentrated by rotary evaporation. The combined products were purified by flash chromatography (1-4 % MeOH in EtOAc, step gradient) to provide 0.77 g of the title compound.
F. I -(R, S)-2-(S)-1- j3- j5-(methyl)-I , 2, 4-oxadiazolylJ-2-amino-S- j(4-methoxy-2, 3, 6-trimethyl-benzenesulphonyl)-guanidinoJ pentan-I-of triJluoroacetate salt:
Compound E (0.74 g) was dissolved in 6.5 mL of dry chloroform and treated with 0.27 mL of triethyl amine and 0.153 mL of acetic anhydride and allowed to stir 4 hours at room temperature. The reaction was diluted with 50 mL toluene and refluxed for approximately 15 hours in a 120°C
oil bath. The volatile solvents were removed by rotary evaporation and the residue was worked up according to method A. Drying over sodium sulfate, concentration by rotary evaporation, and flash chromatography on silica gel eluting with EtOAc provided 0.34 g of a colorless oil. A portion of this material 0.17 g was dissolved in 4 mL of MeOH and chilled to 0°C.
To this solution was added 90 uL of a 4 N solution of KzC03. The reaction stirred two hours and was then partitioned between 40 mL of EtOAc and 5 mL water. The organic layer was washed with saturated sodium chloride solution and dried over sodium sulfate. The ethyl acetate was removed by rotary evaporation and traces of ethyl acetate were removed by rotary evaporation from dichloromethane. The resulting residue was diluted in 1.33 mL of dichloromethane and chilled to 0°C. Trifluoroacetic acid (0.57 mL) was added and the reaction stirred 1.5 hour at 0°C. The solvent was rapidly removed in vacuo and the product was dissolved in dichloromethane and concentrated to dryness by rotary evaporation.
G. I-(R,S)-2-(S)-L-leucyl-N jl-j(3-j5-(methyl)-1,2,4-oxadiazolylJ-hydroxymethylJ-4-j(4-methoxy-2,3,6-trimethyl-benzenesulphonyl)-guanidino)J-butyl)-L-leucine amide:
Compound F
(146 mg) and Acetyl-Leu-Leu-OH (82 mg) were dissolved in 5 mL of dry DMF and treated with 200 uL of DIEA, followed by 30 mg of HBTU. After 5 minutes an additional 100 uL of DIEA
was added and the reaction stirred approximately 15 hours at room temperature.
The reaction was diluted with EtOAc and washed with saturated NaHC03 solution and saturated sodium chloride solution. After removal of the solvent by rotary evaporation the product was purified by preparative C18 reverse phase chromatography (5-60% CH3CN, 0.1% TFA) to provide 122 mg of the title compound.
H. Acetyl-L-leucyl-N jl-j3-j(5-methyl)-1,2,4-oxadiazolyl)carbonyl)-4-j(4-methoxy-2,3,6-trimethyl-benzenesulphonyl)-guanidinoJ-butyl)-L-leucyl amide: N-chlorosuccinimide (45 WO 99/54317 PCT/US99/0$501 mg) and dimethyl sulfide (61 uL) in 2.5 mL of toluene were chilled to 0°C with stirring. Stirred at 0°C for 30 minutes. The mixture was then chilled to ~-25°C in a dry ice/carbon tetrachloride bath, then compound G (100 mg) was added by dropwise addition in a mixture of 2.5 mL of dichloromethane and 1.5 mL of toluene. The reaction stirred at -25 °C
for 3 hours then 100 uL of triethyl amine was added. After 5 minutes the cooling bath was removed, and the reaction stirred 1 hour. The reaction mixture was diluted with EtOAc, and washed with saturated sodium bicarbonate solution and saturated sodium chloride solution. The solution was dried over anhydrous sodium sulfate solution and concentrated to an oil.
I. Acetyl-L-leucyl-N('I-j3-j(5-methyl)-1,2,4-oxadiazolylJcarbonylJ-4-(guanidino)-butyl-Z-leucyl amide: Compound H was taken up in 1.75 mL of TFA and chilled to 0°C. Thioanisole (90 uL) was added and the reaction stirred 1 hour at 0°C, and 4 hours at room temperature. The volatile solvents were removed by rotary evaporation, and residual TFA was removed by adding dichloromethane and concentrating to dryness on the rotovap. Reversed phase C
18 preparative chromatography provided the title compound. FAB MS m/z (M+H)r 509 (CQ-0008).
Example V - Synthesis of Acetyl-L-tyrosinyl-L-valyl-N jl - j2- j(S phenyl)-l, 3, 4-oxadiazolylJcarbonylJ-2-carboxy-ethylJ-L-alanine amide (CQ-0010) A. N'-Benryloxycarbonyl-L Aspartyl(O-t-butyl) N methyl-N methoxy amide: Cbz-L-Aspartic Acid (0-t-butyl) (1.0 g, 2.93 mmole), N,O-dimethyl hydroxyl amine hydrochloride (0.357 g, 3.66 mmole, were suspended in 15 mL of DMF and treated with 1.53 mL
(8.79 mmoles) of DIEA under N~ atmosphere. HBTU (1.22 g, 3.22 mmoles) was added and the reaction stirred approximately 15 hours at room temperature. The reaction mixture was worked up according to general extractive work up method A. Drying over NazS04, rotary evaporation of the solvent and further drying under high vacuum provided 1.1 g as a colorless glassy solid.
B. L-Aspartyl-(O-t-butyl) N methyl-N methoxy amide: Compound A (1 g) was dissolved in 20 mL methanol containing 5% (v/v) formic acid. The solution was deoxygenated with nitrogen bubbling then treated with approximately 200 mg of palladium black.
The reaction stirred under nitrogen for 3 hours, and was then filtered through celite. The celite was washed well with methanol and the filtrates were combined and concentrated by rotary evaporation.

Residual methanol and formic acid were chased off by the addition and rotary evaporation of CHZCIz and 50:50 CHZCIz:hexane. Drying under high vacuum provided 790 mg of an oil.
C. Acetyl-L-tyrosinyl-L-Valyl-L-Alanyl-L-Aspartyl-(O-t-butyl) N methyl-N
methoxy amide: Compound B (150 mg) and Acetyl-Tyr-Val-Ala-OH (230 mg , prepared using S conventional peptide synthesis) were combined and suspended in 10 mL of DMF.
DIEA (305 uL) was added followed by HBTU. Product from normal extractive work up, and the 1 N HCl washes were combined after evaporation and purified by preparative HPLC
chromatography (S -60% CH3CN 0.1 % TFA, over 30 minutes) to provide a lyophilized fraction of 85 mg of 94%
pure material, which was carried on to the anion coupling reaction.
D. Acetyl-L-tyrosinyl-L-valyl-N jl-j2-j(5 phenyl)-1,3,4-oxadiazolylJcarbonylJ

(carboxy-t-butyl)-ethylJ-L-alanine amide: 2-Phenyl-1,3,4,-oxadizaole (i69 mg, 1.16 mmole) was dissolved in 2 mL dry THF, and chilled to -78 C. n-Butyl lithium (510 uL, 2.5 M solution in hexane) was added via syrringe, after 20 minutes compound C (88 mg, 0.145 mmole) was added via syrringe in 3 mL dry THF and the reaction was allowed to warm to room temperature.
After 15 minutes 20 mL of saturated NH4C1 solution was carefully added under nitrogen, and the solution was rapidly stirred for several minutes. The resulting solution was extracted with EtOAc, dried over Na2S0,, and concentrated. The resulting product was dissolved in HZO/
CH3CN and concentrated by freeze-drying. Reverse phase preparative HPLC
chromatography (5-60% CH3CN, 0.1 % TFA, 30 minute gradient) provided 25.8 mg of a colorless powder upon lyophilization.
E. Acetyl-L-tyrosirryl-L-valyl-N jl-j2-j(S phenyl)-1,3,4-oxadiazolylJcarbonylJ-carboxy-ethylJ-L-alanine amide: Compound D (25 mg) was treated with 2 mL of TFA and stirred at room temperature for 2 hours. The TFA was removed on the rotovap, and remaining entrained solvent was removed by adding CH2Clz and CH~CN and evaporating. The crude product was purified by reverse phase HPLC chromatography (5- 60% CH3CN, 0.1%.TFA, 30 minute gradient). Lyophilization of appropriate fractions provided 15.7 mg of a colorless lyophilate. Maldi MS M+Na 659 observed. MS FAB (M+H)' 637.
1 H-NMR: a 0.7? (m, 6H), 1.1-1.2 (m, 3H), 1.74 (s , 3H) 1.9 ( m, 1 H), 2.57 -2.8 (m, 2H), 2.75-3.34 (m, 2H) 4.14 (m, 1 H) 4.3 (m, 1 H), 4.44 (m, 1 H) 5.3 (m, 1 H), 6.61 (m, 2H), 7.01 (m, 2H), 7.70 (m, 3H) 7.73 (m, 2H) 7.74 - 8.00 (m, 2H) 8.1 (m, 2H) 8.78 (m, 1H), 9.13 (bs, 1H) 12.65 (bs, 1H). "C-NMR - d 17.8, 17.9, 19.0, 22.3, 30.6, 34.9, 36.3, 47.5, 52.7, 54.0, 57.0, 114.6, 122.3, 127.2, 129.5, 129.9, 132.9, 155.6, 159.6, 164.9, 169.0, 170.2, 171.1, 171.3, 172.2, 172.3, 183.8.
Example VI -Acetyl-L Aspartyl-Valyl-N (1-~2-((S phenyl)-1,3,4-oxadiazolylJ
carbonyl)-2-(carboxy)-ethyl)-L=glutamyl amide (CQ-0011) A. Acetyl-L-Aspartyl(Ot-Bu)-L-Valyl-L-Glutamyl (O-t-Bu)-L-Aspartyl-(O-t-butyl) N
methyl-N-methoxy amide: Acetyl-Asp(O-t-Bu)-Val-Glu-(O-t-Bu)-OH (0.302 g, 0.586 mmoles, prepared by conventional peptide synthesis) and H-Asp-(O-t-Bu)-N-(CH3)-OCH3 (0.150 g, 0.645 mmole, prepared as in example VIII) were combined in 5 mL of DMF and DIEA (305 uL) was added. HBTU (277 mg) was added. After 2 hours an additional 200 uL of DIEA was added and the reaction was allowed to stir approximately 15 hours at room temperature.
The reaction was worked up according to method A, dried over Na=SO., and concentrated to an oil. Preparative reverse phase chromatography (C18, 5 - 60% CH3CN, 0.1% TFA, 30 minute gradient), and lyophilization of appropriate fractions provided 0.231 g of a colorless lyophilate.
B. Acetyl-L-Aspartyl (O-t-Bu)-Valyl-N ~1-~2-((S phenyl)-1, 3, 4-oxadiazolylJcarborrylJ 2-(carboxy-O-t-butyl)-ethyl)-L-glutamyl(O-t -Bu) amide: 2-Phenyl-1,3,4;
oxadiazole (161 mg, 1.1 mmole) was dissolved in 2 mL dry THF, and chilled to -78 °C. n-Butyl lithium (485 uL, 2.5 M
solution in hexane) was added via syringe, after 20 minutes compound A (100 mg, 0.138 mmole) was added via syringe in 3 mL dry THF and the reaction was allowed to warm to room temperature. After 60 minutes 20 mL of saturated NH4Cl solution was carefully added under nitrogen, and the solution was rapidly stirred for several minutes. The resulting solution was extracted with EtOAc, dried over NazS04 and concentrated. The resulting product was dissolved in HZO/ CH3CN and concentrated by freeze-drying. Reverse phase preparative HPLC
chromatography (5-60% CH,CN, 0.1% TFA, 30 minute gradient) provided 34 mg of a colorless powder upon lyophilization.
C. Acetyl-L Aspartyl-Valyl-N (1-(2-((S pherryl)-1,3,4-oxadiazolylJ carborrylJ-(carboxy)-ethyl)-L-glutamyl amide: Compound B (25 mg) was treated with 2 mL
tnL of TFA
and stirred at room temperature for 5.75 hours. The TFA was removed on the rotovap, and remaining entrained solvent was removed by adding CHZCIZ and CH~CN and evaporating. The crude product was purified by reverse phase HPLC chromatography (5-60% CH3CN, 0.1 % TFA, 30 minute gradient). Lyophilization of appropriate fractions provided 15.1 mg of a colorless lyophilate. Maldi MS M+Na 669 observed. MS FAB (M+H)' 647.
'H-NMR 6 0.73 (m, 6H), 1.75 - 1.95 (m, 2H), 1.82 (s, 3H), 1.88 (m, 2H), 2.40 -2.70 (m, 2H) 2.75 -3.05 (m, 2H), 4.14 (m, 1 H), 4.30 (m, 1 H), 4.58 (m, 1 H), 5.33 (m, 1 H) 7.55 (m, I H) 7.61-7.73 (m, 3H), 8.02 (m, 1H), 8.10 (m, 2H), 8.25 (m, 1H) 8.72 - 8.82 {m, 1H), 12.3 (bs, 3H). "C-NMR a 17.5, 18.9, 22.3, 27.2, 29.8, 30.6, 34.8, 35.5, 49.3, 51.2, 52.7, 57.0, 122.3, 127.2, 129.5, 132.9, 159.6, 164.9, 169.4, 170.4, 170.5, 171.2, 171.3, 173.7, 183.8.
Example VII - General extractive work up Method A
The reaction mixture was diluted with 5-10 volumes of EtOAc and washed three times each with equivalent volumes of 1 N HCl solution, then saturated NaHC03 solution, and finally with saturated NaCI solution.
Example VIII - Inhibitory Activity Against Cathepsin B and L, Papain and Gingipain The enzyme cathepsin B (E.C. 3.4.22.01) was obtained from Calbiochem (San Diego, CA); cathepsin L (E.C. 3.4.22.15) from Athens Research and Technology Inc.
(Athens,GA); and papain (E.C. 3.4.22.02) from Sigma (St. Louis, MO).
Cbz-Phe-Arg-NHMec (-NHMec: 7-(4-methyl)coumarylamide) was obtained from BachemCalifonzia, inc. (Torrance, CA). All other reagents were obtained from Sigma.
The enzymes used in enzyme assays with methylcoumarylamides were activated as described elsewhere (Barnet, et al., Methods Enrymol. 80:535-56I (1981);
Briimme, et al., Biochem. J., 264: 475-481 (1989). Cathepsin L was assayed in 0.34 M sodium acetate buffer, pH
5.5, containing 0.1 % (v/v) Brij 35, 2.5 mM dithiothreitol (DTT) and 5 mM Na2-EDTA.
Cathepsin B was assayed under the same conditions, except that the buffer was adjusted to pH 6.
Papain was assayed in 50 mM sodium phosphate buffer, pH 6.8, containing 0.2 M
sodium chloride, 2 mM DTT, 1 mM Na2-EDTA and 0.025 % Brij 35 (v/v).
Initial velocities of enzymatic reactions were measured spectrofluorometrically (.1~ = 370 nm, ~.~m 460 nm) with a Quanta Master QM1 (Photon Technologies International, South Brunswick, N.l). Stock solutions of the enzymes were diluted into the buffer, equilibrated at room temperature, and preincubated without or with increasing concentrations of inhibitors. The reactions were started by addition of substrate. A total of 4 to 8 inhibitor concentrations were used to determine IC5° values. In all cases the substrate concentrations were much smaller than the IC", value, and the ICso values measured approximated the K; directly (Cheng, et al., Biochemical Pharmacology, 22:3099-3108 (1973)).
Gingipain assay - All assays were carried out in a 96 well microtiter plate reader and cleavage of BAPNA (Na-benzoyl-DL-arginine p-nitroanilide hydrochloride) was detected at 405 nm.
All assays were performed as follows: 180 pl assay buffer (50 mM Tris, 5 nM
CaClz and 10 nM cysteine, at pH 7.6) was mixed with 10 pl gingipain R (RGP). The mixture was incubated for 5 min. at room temperature to reduce and activate RGP. 10 pl of each inhibitor were added at various concentrations. These mixtures were incubated for 10 min. at room temperature to allow the inhibitors to complex with RGP. SO pl of 10 mM BAPNA
substrate was added. A two minute assay was performed with a final volume of 250 pl, and a final BAPNA concentration of 2 mM.
2 mM BAPNA was sufficient excess of substrate such that substrate depletion did not occur within a 10 minute assay time.. For this reason, two minute assays were performed whereby the Vm,~ in mOD/min change in absorbance at 405 nm was used as the initial velocity reading. In order to titrate RGP against leupeptin and to determine %
activity, these velocity readings were transformed on a percent scale where the 100% control contained no inhibitor.
The initial velocity values were also entered into Graphpad Prism regression program along with the various inhibitor concentrations to obtain the IC,° values. All data represents the minimum of duplicates, and at times triplicate scts.
Assay results are presented in Table 3. As shown, CM-0019B is an inhibitor of papain and cathepsin L and more selective against cathepsin B than is leupeptin.
Compound CQ-0002, which shares the same recognition sequence {Leu-Leu-Arg) with the broad spectrum inhibitor leupeptin, is nearly as potent as leupeptin versus cathepsin B, but surpisingly has.,a much higher degree of specificity. In addition, compound CQ-0002 inhibits gingipain R with a potency equivalent to that of leupeptin. Compounds CQ-0004 and CQ-0008 are also potent and selective cathepsin L inhibitors.
Table 3.
K; (nM] Values for Cysteine Protease Inhibitors COMPOUND PAPAW CATHEPSIN.B'CATHEPSIN GINGIPAIN
L' R' Leupeptin 1.0 t 0.06 6.1 t 1.2 0.62 t 0.10 20.8 (IC50) CM-0019Bb 85 3,000 100 CQ-0002 1,2001280 324 t 46 6.0 f 0.98 28 (IC50) CQ-0004 25600 t 27200 t 190061 t 14 CQ-0008 8590 t 18601240 t 182 7.13 t 0.32 ' Human enzyme.
b "B"denotes remake of larger quantities of corresponding CQ number.
Example IX - Inhibitory Activity Against Caspases Assay for ICE inhibition To examine the ability of the caspase family inhibitors, CQ-0010 and CQ-0011, to inhibit human IL-1 (3 production, two different assays were employed. In the first, the human monocytic cell line, THP-1, was stimulated with E. colt lipopolysaccharide (LPS serotype 0127-88; Sigma Chemical Co., St. Louis, MO) in the presence and absence of the inhibitors.
This cell line synthesizes and secretes IL-1 ~i and TNFa as well as other cytokines upon LPS
stimulation. The second assay used freshly-isolated human whole blood similarly stimulated with LPS.
THP-1 assay: Two x 106 THP-1 cells were added to 24 well plates in 1 ml RPMI
supplemented with 1% FCS, glutamine and 5 x 10'5 M mercaptoethanol. Two-fold serial dilutions of the inhibitors, CQ-0010, CQ-0011 and the commmercially available Ac-YVAD-CHO (Biomol Research Laboratories Inc., Plymouth Meeting, PA), were preincubated with the cells for 15 min at 37°C. LPS was then added to a final concentration of 1 ug/ml and the plates incubated for 4 hr at 37°C. All incubations were carried out in a humidified incubator with 5%
COZ in air.
Supernatants were harvested after 4 hr and assayed by ELISA for the presence of TNFa and IL-1 (3 using commercially available kits (PerSeptive Biosystems, Framingham, MA and R&D Systems, Minneapolis, MN, respectively).
Human whole blood assay: Heparinized whole blood (19.7 U heparin per ml) from healthy volunteers was collected and dispensed into 12 x 75 mm polystyrene tubes (0.25 ml per tube). The inhibitors, CQ-0010, CQ-0011 and Ac-YVAD-CHO were dissolved in DMSO, then diluted and added to the tubes in 0.25 ml and preincubated with the blood for 15 min at 37°C.
LPS was then added to a final concentration of 10 or 100 ug/ml.
The tubes were loosely-capped and incubated in a water bath for 4 hr at 37°C after which they were immersed briefly in an ice-water bath. Supernatants were harvested by centrifugation and stored at -70°C. The presence of TNFa and IL-1 (i was detected by commercially-available ELISA kits.
Assay for other caspase and granryme B inhibition Inhibition constants were measured photometrically for YAMA (caspase 3), Lap3 (caspase 7), FLICE (caspase 8), Mch2 (caspase 6) and granzyme B. The buffer used for all enzymes consisted of 50 mM Hepes, 100 mM sodium chloride, 10% (v/v) sucrose, 0.1% (v/v) CHAPS and 10 mM dithiothreitol (DTT). In the case of granzyme B, only 1 mM DTT
was used.
Enzymes were incubated at 37°C for 10 minutes in 100 pL well plates and synthetic substrate and inhibitor were added simultaneously. Final substrate concentration was 20 ~M in all cases. The synthetic substrate Ac-DEVD-pNA was used for all caspases and Succ-AAPD-pNA was used for graazyme B. The appearance of product was monitored over 10 minutes at 410 nm using a Spectromax 340 and ICS curves were calculated from the initial slopes at varying inhibitor concentrations and inhibition constants were calculated.
The results are shown in Table 4.

Table 4.
Inhibition of Caspases -Comparison with Ac-YVAD-CHO

Caspases Ac-YVAD-CHO Ac-YVAD-het Ac-DVED-het (CQ-0010) (CQ-0011) yAMA (CPP32, 20 3.3 s0.1 Caspase 3) Mch2 (Caspase 100 33 6.7 6) Lap3 Not Active Not Active 50.03 (slow) (Mch3, Caspase 7) FLICE 3.7 s0.02 50.03 (slow) (MchS, Caspase 8) ICE 0.3b 0.3b 3b (Caspase 1) 0.3 - 0.5' 0.3 - 0.5' Granzyme Not Active Not Active Not Active ' Values given are lt; Iri ilM, unless Vmarwmo utumamu.
IC50 (i1M) values of reduction of IL-1 p release from THP-1 cell line.
' IC50 (lIM) values of reduction of IL-1 ~i release in whole blood assay.
The results indicate that CQ-0010 is an extremely potent and specific inhibitor of IL-1 ~i production, capable of almost completely inhibiting the production of this cytolcine at 5 pM
(Figure 1) while having no dose-dependent effect on levels of TNFa produced (results not shown). The IC~o of CQ-0010 was estimated from these dose curves to be 0.3 IIM. CQ-0011 also inhibited IL 1 p production but with approximately 10-fold less potency (Figure 1; Table 4).
In the whole blood assay, CQ-0010 was again equipotent to Ac-YVAD-CHO with an ICso of 0.3-0.5 pM (Figures 2a and b).
It should be noted that CQ-0010 was equipotent to the aldehyde equivalent (Ac-YVAD-CHO) in inhibiting ICE, but showed improved inhibition against FLICE with a K;
of s 20 nM.

WO 99/54317 PCT/US99/0850i Compound CQ-0011 is a potent inhibitor of Lap3 and FLICE. The compounds are selective and potent caspase inhibitors as shown by their inactivity with respect to granryme B.

The following references are incorporated herein:
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Claims

We claim:
1. A cysteine protease inhibitor of formula (I):
wherein Z is a cysteine protease binding moiety;
R1 is alkyl or alkenyl optionally substituted with 1-3 halo or hydroxy;
alkylamino, dialkylamino, alkyldialkylamino; or cycloalkyl, alkylcycloalkyl, alkenylcycloalkyl, (C5-C12) aryl, (C5-C12)arylalkyl or (C5-C12)arylalkenyl optionally comprising 1-4 heteroatoms selected from N, O and S, and optionally substituted with halo, cyano, nitro, haloalkyl, amino, aminoalkyl, dialkylamino, alkyl, alkenyl, alkynyl, alkoxy, haloalkoxy, carboxyl, carboalkoxy, alkylcarboxamide, (C5-C6)aryl, -O-(C5-C6)aryl, arylcarboxamide, alkylthio or haloalkylthio; and Y and X are independently O, S or N, said N being optionally substituted with alkyl or alkenyl optionally substituted with 1-3 halo atoms; (C5-C6) aryl, arylalkyl or arylalkenyl optionally comprising 1-3 heteroatoms selected from N, O and S, and optionally substituted with halo, cyano, nitro, haloalkyl, amino, aminoalkyl, dialkylamino, alkyl, alkenyl, alkynyl, alkoxy, haloalkoxy, carboxyl, carboalkoxy, alkylcarboxamide, arylcarboxamide, alkylthio or haloalkylthio;
wherein at least one of Y or X is N; or a pharmaceutically acceptable salt thereof.
2. An inhibitor of claim 1 wherein Z is of the formula (II):
wherein AA1, AA2, AA3, AA4 and AA5 are independently an amino acid residue or amino acid residue mimetic; a direct bond or absent; and R4 and R4' are independently -C(O)R5, -C(O)NHR5, -S(O)2R5, -C(O)R5, -CR5 or R5, where R5 is H, alkyl, alkenyl or alkynyl optionally substituted with halo, cyano, nitro, haloalkyl, amino, aminoalkyl, dialkylamino, haloalkoxy, carboxyl, carboalkoxy or alkylcarboxamide;
cycloalkyl, alkylcycloalkyl, (C5-C12) aryl or (C5-C12)arylalkyl optionally comprising 1-4 heteroatoms selected from N, O and S, and optionally substituted with halo, cyano, nitro, haloalkyl, amino, aminoalkyl, dialkylamino, haloalkoxy, carboxyl, carboalkoxy, alkylcarboxamide, alkyl, alkenyl, alkynyl or (C5-C12)aryl; or absent; or together R4 and R4' form a ring comprising 5-7 atoms selected from C, N, S and O.
3. An inhibitor of claim 2 wherein Z comprises a pentapeptidyl binding moiety.
4. An inhibitor of claim 2 wherein Z comprises a tetrapeptidyl binding moiety.
5. An inhibitor of claim 2 wherein Z comprises a tripeptidyl binding moiety.
6. An inhibitor of claim 2 wherein Z comprises a dipeptidyl binding moiety.
7. An inhibitor of claim 2 wherein the amino acids are selected from arginine or an arginine mimetic, proline; aspartic and glutamic acid and the aryl and alkyl esters thereof; alanine and glycine optionally substituted at the .alpha.-carbon or .alpha.-nitrogen with alkyl, cycloalkyl or aryl;
leucine, isoleucine; cysteine optionally substituted at the sulfur atom with alkyl, alkenyl or phenyl optionally substituted with halo, cyano, nitro, haloalkyl, amino, aminoalkyl, dialkylamino, alkyl, alkoxy, haloalkoxy, carboxyl, carboalkoxy, alkylcarboxamide, arylcarboxamide, alkylthio or haloalkylthio; phenylalanine, homo-phenylalanine, dehydro-phenylalanine, indoline-2-carboxylic acid; tetrahydroisoquinoline-2-carboxylic acid optionally substituted with halo, cyano, nitro, haloalkyl, amino, aminoalkyl, dialkylamino, alkyl, alkoxy, haloalkoxy, carboxyl, carboalkoxy, alkylcarboxamide, arylcarboxamide, alkylthio or haloalkylthio; tyrosine, serine or threonine optionally substituted with alkyl or aryl; tryptophan, histidine, methionine, valine, norvaline, norleucine, octahydroindole-2-carboxylic acid;
asparagine, glutamine and lysine optionally substituted at the nitrogen atom with alkyl, alkenyl, alkynyl, alkoxyalkyl, alkylthioalkyl, alkylaminoalkyl, dialkylaminoalkyl, carboxyalkyl, alkoxycarbonyl alkyl or cycloalkyl, bicycloalkyl, cycloalkyl alkyl, bicycloalkyl alkyl or fused aryl-cycloalkyl alkyl optionally comprising 1 or more heteroatoms selected from N, O and S.
8. An inhibitor of claim 2 wherein AA, is of the formula (IIIa):
wherein X' is CR2' or N; and R2, R2' and R2" are independently H; alkyl or alkenyl optionally substituted with 1-3 halo, hydroxy, thio, alkylthio, amino, alkylamino, dialkylamino, alkylguanidinyl, dialkylguanidinyl, guanidinyl; -RCOR', -RCOOR', -RNR'R"R° or -RC(O)NR'R" where R is alkyl or alkenyl, and R', R" and R° are independently H, alkyl, alkenyl, cycloalkyl or (C5-C6)aryl; or cycloalkyl, alkylcycloalkyl, alkenylcycloalkyl, alkyl-oxyaryl, alkyl-thioaryl, (C5-C12) aryl, (C5-C12)arylalkyl or (C5-C12)arylalkenyl optionally comprising 1-4 heteroatoms selected from N, O
and S, and optionally substituted with hydroxy, halo, cyano, nitro, haloalkyl, amino, aminoalkyl, dialkylamino, amidine, alkylamidine, dialkylamidine, alkyl, alkenyl, alkynyl, alkoxy, haloalkoxy, carboxyl, carboalkoxy, alkylcarboxamide, (C5-C6)aryl, -O-(C5-C6)aryl, arylcarboxamide, alkylthio or haloalkylthio; or R2 and R2' together with X' form a ring comprising 4-7 atoms selected from C, N, S and O, said ring optionally subsitituted with hydroxy, halo, cyano, nitro, haloalkyl, amino, aminoalkyl, dialkylamino, amidine, alkylamidine, dialkyl amidine, alkyl, alkenyl, alkynyl, alkoxy, haloalkoxy, carboxyl, carboalkoxy, alkylcarboxamide, (C5-C6)aryl, -O-(C5-C6)aryl, arylcarboxamide, alkylthio or haloalkylthio.
9. An inhibitor of claim 8 wherein AA2 is of the formula (IIIb):
~
or selected from a compound of formulas IV to XXIV:

wherein X" is CR'3 or N;
R3, R'3 and R"3 are independently H; alkyl or alkenyl optionally substituted with 1-3 halo, hydroxy, thio, alkylthio, amino, alkylamino, dialkylamino, alkylguanidinyl, dialkylguanidinyl, guanidinyl; -RCOR', -RCOOR' or -RC(O)NR'R" where R is alkyl or alkenyl, and R' and R" are independently H, alkyl, alkenyl, cycloalkyl or (C5-C6)aryl;
or cycloalkyl, alkylcycloalkyl, alkenylcycloalkyl, alkyl-oxyaryl, alkyl-thioaryl, (C5-C12) aryl, (C5-C12)arylalkyl or (C5-C12)arylalkenyl optionally comprising 1-4 heteroatoms selected from N, O and S, and optionally substituted with hydroxy, halo, cyano, nitro, haloalkyl, amino, aminoalkyl, dialkylamino, amidine, alkylamidine, dialkylamidine, alkyl, alkenyl, alkynyl, alkoxy, haloalkoxy, carboxyl, carboalkoxy, alkylcarboxamide, (C5-C6)aryl, -O-(C5-C6)aryl, arylcarboxamide, alkylthio or haloalkylthio;
m is 0, 1 or 2;
n is 0, 1 or 2;
G is -C(O)-, -NHC(O)-, -S(O)2-, -OC(O)-, -C- or a direct bond;
R6, R7, R'6, R'7 are independently H, alkyl, alkenyl, halo, alkoxy, carboxyl, carboalkoxy, amino, aminoalkyl, dialkylamino; cycloalkyl, (C3-C6) aryl or (C5-C6) arylalkyl optionally comprising 1-3 heteroatoms selected from N, O and S, and optionally substituted with alkyl, alkenyl, alkynyl, halo, cyano, nitro, haloalkyl, haloalkoxy, amino, alkylamino, dialkylamino, alkoxy, haloalkoxy, carboxyl, carboalkoxy, alkylcarboxamide, alkylthio, guanidine, alkylguanidine, dialkylguanidine, amidine, alkylamidine or dialkylamidine; and U, V, W and Y' are independently or together N, C, C(O), N(R9) where R9 is H, alkyl, halo, alkoxy, carboalkoxy, cycloalkoxy, carboxyl, alkylthio, amino, alkylamino, dialkylamino; or aryl, fused aryl or cycloalkyl optionally comprising 1 or more heteroatoms selected from O, S
and N, and optionally subsituted with halo or alkyl; N(R10) where R10 is H, alkyl, alkenyl or cycloalkyl, aryl, arylalkyl or fused aryl-cycloalkyl optionally comprising 1-4 heteroatoms selected from N, O and S, and optionally substituted with alkyl, alkenyl, alkynyl, halo, cyano, nitro, haloalkyl, haloalkoxy, amino, alkylamino, dialkylamino, alkoxy, haloalkoxy, carboxyl, carboalkoxy, alkylcarboxamide, alkylthio, guanidine, alkylguanidine, dialkylguanidine, amidine, alkylamidine or dialkylamidine; or C(R11)(R12) where R11 and R12 are independently or together H, alkyl, alkythio, alkythioalkyl or cycloalkyl, alkylcycloalkyl, phenyl or phenyl alkyl optionally subsituted with guanidine, carboalkoxy, hydroxy, haloalkyl, alkylthio, alkylguanidine, dialkylguanidine, amidine, alkylamidine or dialkylamidine.
10. An inhibitor of claim 9 wherein AA3, AA4 and AA3 are a direct bond or absent; or an amino acid selected from arginine or an arginine mimetic, proline; aspartic and glutamic acid and the aryl and alkyl esters thereof; alanine or glycine optionally substituted at the .alpha.-carbon or .alpha.-nitrogen with alkyl, cycloalkyl or aryl; leucine, isoleucine; cysteine optionally substituted at the sulfur atom with alkyl, alkenyl or phenyl optionally substituted with halo, cyano, nitro, haloalkyl, amino, aminoalkyl, dialkylamino, alkyl, alkoxy, haloalkoxy, carboxyl, carboalkoxy, alkylcarboxamide, arylcarboxamide, alkylthio or haloalkylthio; phenylalanine, homo-phenylalanine, dehydro-phenylalanine, indoline-2-carboxylic acid;
tetrahydroisioquinoline-2-carboxylic acid optionally substituted with halo, cyano, nitro, haloalkyl, amino, aminoalkyl, dialkylamino, alkyl, alkoxy, haloalkoxy, carboxyl, carboalkoxy, alkylcarboxamide, arylcarboxamide, alkylthio or haloalkylthio; tyrosine, serine or threonine optionally substituted with alkyl or aryl; tryptophan, histidine, methionine, valine, norvaline, norleucine, octahydroindole-2-carboxylic acid; asparagine, glutamine and lysine optionally substituted at the nitrogen atom with alkyl, alkenyl, alkynyl, alkoxyalkyl, alkylthioalkyl, alkylaminoalkyl, dialkylaminoalkyl, carboxyalkyl, alkoxycarbonyl alkyl or cycloalkyl, bicycloalkyl, cycloalkyl alkyl, bicycloalkyl alkyl or fused aryl-cycloalkyl alkyl optionally comprising 1 or more heteroatoms selected from N, O and S;
11. An inhibitor of claim 8 wherein X' is N.
12. An inhibitor of claim 9 wherein X" is N.
13. An inhibitor of claim 8 wherein X' is CR'2, and R'1 is H.
14. An inhibitor of claim 9 wherein X" is CR'3, and R'3 is H.

15. An inhibitor of claim 10 wherein 2 is a calpain binding moiety.
16. An inhibitor of claim 15 wherein R2 is CH3SCH2CH2-, HOOC(CH2)2CH2-, cyclohexyl-CH2-, imidazolyl-CH2, (CH3)2CHCH2-, (CH3)2CH-, CH3CH2CH2- or CH3(CH2)2CH2-; benzyl optionally substituted with alkoxy, OH or -O-ben2yl; H2NC(=+NH2)NHCH2CH2CH2-;
-R'-C(=+NH2)NH2; -R'-NHC(=+NR")NR°; or -R'-NR"R° where R' is cycloalkyl, aryl or arylalkyl optionally substituted with one or more heteroatoms selected from N, S or O
alkyl; and R" and R° are alkyl or cycloalkyl.
17. An inhibitor of claim 16 wherein R3 is -CH2-benzyl, benzyl, (CH3)3C-, (CH3)3CCH2-, (CH3)2CH-, CH3(CH2)2CH2-, CH3CH2CH(CH3)- or (CH3)2CHCH2-.
18. An inhibitor of claim 17 wherein R3 is benzyl, isoquinolinyl, quinolinyl, naphthyl or HOOCCH2C(CH2CH(CH3)2)-.
19. An inhibitor of claim 17 wherein R4 is Cbz wherein the phenyl is optionally substituted with nitro.
20. An inhibitor of claim 17 wherein R4 is toluenesulfonyl, methanesulfonyl, FMOC or (+)-menthyloxy-CO-.
21. An inhibitor of claim 16 wherein AA3 is leucine, AA4 and AA5 are direct bonds or absent, and R5 is alkyl.
22. An inhibitor of claim 7 wherein Z is R4-Leu-Leu-Leu-;
R4-Leu-Leu-;
R4-Leu-Leu-Phe-;
R4-Leu-Abu-;

R4-Val-Phe-;
R4-Leu-Leu-Nle-;
R4-Ala-t-BuGly-Val-;
R4-t-BuGly-Val-;
R4-Leu-Leu-Met-; or R4-Leu-Nle-.
23. An inhibitor of claim 7 wherein Z is Cbz-Leu-Nle-; or Cbz-Leu-Val-.
24. An inhibitor of claim 10 wherein Z is a cysteine cathepsin binding moiety.
25. An inhibitor of claim 24 wherein R2 is CH3-, (CH3)2CH-, (CH3)2CHCH2-, CH3(CH2)2CH2-, CH3CH(-O-benzyl)- or benzyl-S-CH2-; benzyl or -CH2-benzyl optionally substituted with OH ar -OR' where R' is alkyl or aryl; H2NC(=+NH2)NHCH2CH2CH2-;
-R'-C(=+NH2)NH2; -R'-NHC(=+NR")NR°; or -R'-NR"R° where R' is cycloalkyl, aryl or arylalkyl optionally substituted with one or more heteroatoms selected from N, S or O
alkyl; and R" and R° are alkyl or cycloalkyl.
26. An inhibitor of claim 25 wherein R3 is H, (CH3)2CH-, (CH3)2CHCH2-, CH3(CH2)2CH2-, benzyl optionally substituted with hydroxy and halo; (naphthyl)-CH2-;
H2N(CH2)3CH2-, H2N(CH2)2CH2-, H2NC(=+NH2)NHCH2CH2CH2-; -R'-C(=+NH2)NH2; -R'-NHC(=+NR")NR°; or -R'-NR"R° where R' is cycloalkyl, aryl or arylalkyl optionally substituted with one or more heteroatoms selected from N, S or O alkyl; and R" and R° are alkyl or cycloalkyl.
27. An inhibitor of claim 24 wherein Z is a cathepsin B binding moiety.
28. An inhibitor of claim 27 wherein R2 and R3 are independently benzyl, -CH2-benzyl, H2N(CH2)3CH2-, H2N(CH2)2CH2-, H2NC(=+NH2)NHCH2CH2CH2-; -R'-C(=+NH2)NH2;
-R'-NHC(='NR")NR°; or -R'-NR"R° where R' is cycloalkyl, aryl or arylalkyl optionally substituted with one or more heteroatoms selected from N, S or O alkyl; and R"
and R° are alkyl or cycloalkyl.
29. An inhibitor of claim 27 or 28 wherein AAA is Ile or Leu.
30. An inhibitor of claim 28 wherein -AA2-AA1- are -Phe-hPhe-;
-Arg-hPhe-;
-Arg mimetic-hPhe-;
-Lys-hPhe-; or -Orn-hPhe.
31. An inhibitor of claim 24 wherein Z is a cathepsin L, O, K, or H binding moiety.
32. An inhibitor of claim 31 wherein Z is a cathepsin L binding moiety.
33. An inhibitor of claim 32 wherein R3 is benzyl or (CH3)2CHCH2-.
34. An inhibitor of claim 32 or 33 wherein R2 is -CH2-benzyl.
35. An inhibitor of claim 24 wherein Z is a cathepsin S binding moiety.
36. An inhibitor of claim 35 wherein R2 and R3 are alkyl.
37. An inhibitor of claim 36 wherein R2 and R3 are independently (CH3)2CH-, (CH3)2CHCH2- or CH3(CH2)2CH2-.
38. An inhibitor of claim 35 wherein R3 is benzyl, (CH3)2CHCH2- or (CH3)2CH-.

39. An inhibitor of claim 35 or 38 wherein R2 is -CH2-benzyl.
40. An inhibitor of claim 39 wherein AA3, AA4 and AA5 are direct bonds or absent.
41. An inhibitor of claim 40 wherein R5 is benzyl, isoquinolinyl, quinolinyl, naphthyl or HOOCCH2C(CH2CH(CH3)2)-.
42. An inhibitor of claim 41 wherein R4 is Cbz.
43. An inhibitor of claim 31 wherein Z is a cathepsin H binding moiety.
44. An inhibitor of claim 43 wherein Z is R4-hPhe-; or HCl~hPhe-.
45. An inhibitor of claim 31 wherein Z is a cathepsin K binding moiety.
46. An inhibitor of claim 45 wherein R3 is benzyl, (CH2)2CHCH2- or (CH3)2CH-.
47. An inhibitor of claim 45 or 46 wherein AA3 is Gly; and AA4 is Val or D-Val.
48. An inhibitor of claim 7 wherein Z is a cathepsin K binding moiety; and AA1 is Arg, Arg mimetic or hPhe;
AA2 is Pro;
AA3 is Gly; and AA4 is Val or D-Val.
49. An inhibitor of claim 7 wherein Z is a cathepsin K binding moiety; and is R4-Pro-AA1-;

R4-Gly-Pro-AA1-;
R4-Val-Gly-Pro-AA1;
D-Val-Gly-Pro-AA1-; or R4-D-Val-Gly-Pro-AA1; where AA1 is Apa, Arg or Arg mimetic, or hPhe.
50. An inhibitor of claim 24 wherein Z is R4-AA3-Leu-hPhe-;
R4-AA3-Phe-hPhe-; or R1-AA3-Val-hPhe-;
where AA3 is Gly, Val, D-Val, a direct bond or absent.
51. An inhibitor of claim 24 wherein Z is Mu-Val-hPhe-.
52. An inhibitor of claim 10 wherein Z is a caspase binding moiety.
53. An inhibitor of claim 52 wherein R2 is -RCOOR'.
54. An inhibitor of claim 53 wherein R is -CH2- and R' is H.
55. An inhibitor of claim 53 wherein AA3 and AA4 are amino acid residues and AA5 is a direct bond.
55. An inhibitor of claim 55 wherein Z is an interleukin-1.beta. converting enzyme binding moiety.
57. An inhibitor of claim 56 wherein AA4 is optionally substituted tyrosine or leucine.
58. An inhibitor of claim 57 wherein AA3 is valine, glutamate or an ester thereof.

59. An inhibitor of claim 58 wherein R3 is -CH3 or (CH3)2CH-.
60. An inhibitor of claim 56 wherein R3 is -CH3 or imidazolyl-CH2-; AA3 is valine or glutamate; and R5 is -CH3.
61. An inhibitor of claim 7 wherein Z is an interleukin-1.beta. converting enzyme binding moiety, and is R4-AA5-AA4-AA3-Pro-AA1; where AA1 is Asp or Asp ester.
62. An inhibitor of claim 61 wherein -AA5-AA4-AA3- is -Ala-;
-Glu-;
-Val-;
-Tyr-Ala-;
-Tyr-Glu-;
-Tyr-Val-;
-Leu-Ala-;
-Leu-Glu-; or -Leu-Val-.
63. An inhibitor of claim 10 wherein Z is an interleukin-1.beta. converting enzyme binding moiety and AA2 is of the formula (VI);
wherein X" is CR'3;
R2 is -RCOOR' where R is alkyl or alkenyl, and R' is H, alkyl, alkenyl, cycloalkyl or (C5-C6) aryl.
64. An inhibitor of claim 63 wherein R3 and R'3 are H.

65. An inhibitor of claim 63 wherein AA3, AA4 and AA5 are direct bonds or absent, and R2 is -RCOOH where R is -CH2-.
66. An inhibitor of claim 65 wherein R6 is phenyl or benzyl substituted with halo.
67. An inhibitor of claim 66 wherein R5 is benzyl, isoquinolinyl, quinolinyl, naphthyl or HOOCCH2C(CH2CH(CH3)2)-.
68. An inhibitor of claim 53 wherein Z is a YAMA binding moiety, where R is -CH2- and AA4 is Asp or an ester thereof.
69. An inhibitor of claim 68 wherein AA3 is optionally substituted glutamine, or glutamic acid or an ester thereof.
70. An inhibitor of claim 69 wherein R2 is (CH3)2CH- or CH3SCH2CH2-.
71. An inhibitor of claim 53 wherein Z is a FLICE binding moiety, where R2 is -CH2- and AA4 is optinally substituted lysine.
72. An inhibitor of claim 71 wherein AA3 is glutamic acid.
73. An inhibitor of claim 72 wherein R3 is (CH3)2CH-.
74. An inhibitor of claim 10 wherein Z, is a viral or microbial cysteine protease binding moiety.
75. An inhibitor of claim 74 wherein Z is a gingipain binding moiety.
76. An inhibitor of claim 75 wherein Z is a gingipain K binding moiety.

77. An inhibitor of claim 76 wherein R2 is RNR'R"R° where R' is H; R"
and R° are H or alkyl.
78. An inhibitor of claim 75 wherein Z is a gingipain R binding moiety.
79. An inhibitor of claim 78 wherein R2 is H2NC(=+NH2)NHCH2CH2CH2-;
-R'-C(=+NH2)NH2; -R'-NHC(=+NR")NR°; or -R'-NR"R° where R' is cycloalkyl, aryl or arylalkyl optionally substituted with one or more heteroatoms selected from N, S or O
alkyl; and R" and R° are alkyl or cycloalkyl.
80. An inhibitor of claim 7 wherein Z is a gingipain binding moiety, and AA2 is proline.
81. An inhibitor of claim 80 wherein Z is R4-Leu-Pro-AA1-, where AA1 is arginine or an arginine mimetic.
82. An inhibitor of claim 74 wherein Z is a human coronavirus protease binding moiety, and R2 is H2NC(=+NH2)NHCH2CH2CH2-; -R'-C(=+NH2)NH2; -R'-NHC(=+NR")NR°; or -R'-NR"R° where R' is cycloalkyl, aryl or arylalkyl optionally substituted with one or more heteroatoms selected from N, S or O alkyl; and R" and R° are alkyl or cycloalkyl.
83. An inhibitor of claim 82 wherein R3 is (CH3)2CH-, (CH3)2CHCH2- or CH3(CH2)2CH2-;
AA3 is Asp or an ester thereof; Leu, Arg or Arg mimetic, or direct bond;
AA4 and AA5 are direct bonds or absent; and R5 is alkyl.
84. An inhibitor of claim 74 wherein Z is a hepatitis A virus 3C proteinase binding moiety, and R2 is -RC(O)NR'R" where R' and R" are H or -CH3; or RCOOR' where R' is CH3;
and AA3 and AA4 are amino acid residues.
85. An inhibitor of claim 84 wherein AA4 is Leu.
86. An inhibitor of claim 85 wherein R3 is -CH3 and AA3 is Ala.
87. An inhibitor of claim 7 wherein Z is a hepatitis A virus 3C proteinase binding moiety, and is R4-Leu-AA3-Thr-Gln-;
R4-Trp-AA3-Thr-Gln-;
R4-Val-AA3-Thr-Gln-;
R4-Ile-AA3-Thr-Gln-; or R4-D-Leu-AA3-Thr-Gln-;
where AA3 is Arg or Arg mimetic.
88. An inhibitor of claim 74 wherein Z is an Ad2 23K protease binding moiety, and R2 and R3 are H;
AA3 is alanine;
AA4 is leucine;
AA5 is a direct bond; and R4 is absent.
89. An inhibitor of claim 74 wherein Z is a human rhinovirus 3C protease binding moiety, and R2 is RCOOR' where R is -CH2-;
R3 is benzyl; and AA3 is leucine or a direct bond.

90. An inhibitor of claim 74 wherein Z is a human rhinovirus 3C protease binding moiety, and R2 is -RC(O)NR'R" where R' and R" are H or -CH3; or RCOOR' where R' is -CH, or -CH2CH3; or X' is N and R2 is -CH3.
91. An inhibitor of claim 74 wherein Z is human picornain 2A protease.
92. An inhibitor of claim 81 wherein R3 is -CH(OR')CH3 where R' is H, alkyl or aryl.
93. An inhibitor of claim 92 wherein R2 is a hydrophobic side chain.
94. An inhibitor of claim 7 wherein Z is a human picornain 2A protease binding moiety, and is R4-Ala-Ala-Pro-Val-; or R4-Ala-Ala-Pro-Ala-.
95. An inhibitor of claim 10 wherein Z is a protozoan protease binding moiety.
96. An inhibitor of claim 95 wherein Z is a Trypanosoma, Schistosoma or Leishmania protease binding moiety.
97. An inhibitor of claim 96 wherein R2 is benzyl optionally subsituted with OH;
H2NC(=+NH2)NHCH2CH2CH2-; -R'-C(=+NH2)NH2; -R'-NHC(=+NR")NR°; or -R'-NR"R°
where R' is cycloalkyl, aryl or arylalkyl optionally substituted with one or more heteroatoms selected from N, S or O alkyl; and R" and R° are alkyl or cycloalkyl.
98. An inhibitor of claim 97 wherein R3 is benzyl, (CH3)2CHCH2- or (CH3)2CH-;
and AA3 is Phe, Leu, Pro or a direct bond.

99. An inhibitor of claim 98 wherein R4 is Boc or Suc.
100. An inhibitor of claim 95 wherein Z is a Plasmodium protease binding moiety.
101. An inhibitor of claim 100 wherein R2 is (CH3)2CH-; -CH2-benzyl, benzyl or phenyl optionally substituted with hydroxyl; alkylimidazoyl; H2NC(=+NH2)NHCH2CH2CH2-;

-R'-C(=+NH2)NH2; -R'-NHC(=+NR")NR°; or -R'-NR"R° where R' is cycloalkyl, aryl or arylalkyl optionally substituted with one or more heteroatoms selected from N, S or O alkyl; and R" and R° are alkyl or cycloalkyl.
102. An inhibitor of claim 101 wherein R3 is benzyl, (CH3)2CHCH2-, (CH3)2CH-, HOCH2- or - CH2OR'.
103. An inhibitor of claim 100 wherein Z is R4-Phe-Arg-;
R4-Phe-(arginine mimetic)-;
R4-Val-Leu-(arginine mimetic)-;
R4-Phe-Lys-;
R4-Leu-hPhe-;
R4-Val-Leu-Arg-;
R4-Phe(e-Z)-Lys-;
R4-Phe-Val-; or R4-Phe-Ser(OBzl)-.
104. An inhibitor of claim 100 wherein Z is R4-Phe-AA1-; or R4-Leu-AA1-;
wherein AA1 is optionally substituted lysine.

105. An inhibitor of claim 104 wherein R4 is morpholino.
106. An inhibitor of claim 104 wherein R4 is Cbz.
107. A method of inhibiting the enzymatic activity of one or more cysteine proteases comprising contacting a protease with an inhibitory amount of a compound of claim 1.
108. A method of inhibiting the enzymatic activity of one or more cysteine proteases comprising contacting a protease with an inhibitory amount of a compound of claim 10.
109. A method of inhibiting the enzymatic activity of a calpain cysteine protease comprising contacting a protease with an inhibitory amount of a compound of claim 15.
110. A method of inhibiting the enzymatic activity of a cysteine cathepsin comprising contacting the protease with an inhibitory amount of a compound of claim 24.
111. A method of inhibiting the enzymatic activity of a caspase comprising contacting the protease with an inhibitory amount of a compound of claim 52.
112. The method of claim 111 wherein the caspase is human interleukin-1.beta.
converting enzyme.
113. A method of inhibiting the enzymatic activity of a viral or microbial cysteine protease comprising contacting the protease with an inhibitory amount of a compound of claim 74.
114. The method of claim 113 wherein the cysteine protease is human coronavirus.
115. The method of claim 113 wherein the microbial cysteine protease is gingipain.

116. A method of inhibiting the enzymatic activity of a protozoan cysteine protease comprising contacting the protease with an inhibitory amount of a compound of claim 95.
117. The method of claim 116 wherein the protozoan protease is a Trypanosoma, Schistosoma or Leishmania protease.
118. The method of claim 116 wherein the protozoan protease is a Plasmodium protease.
119. A method of inhibiting the enzymatic activity of cancer procoagulant comprising contacting the protease with an inhibitory amount of a compound of claim 1.
120. A method of inhibiting the enzymatic activity of cysteine proteases associated with apoptosis in pathological states comprising contacting the proteases with an inhibitory amount of a compound of claim 1.
121. A method of inhibiting cancer cell growth or tumor progression or tumor metastasis or invasion, by inhibiting the enzymatic activity of cysteine proteases associated with such growth or progession, comprising contacting such protease with an inhibitory amount of a compound of claim 1 or 2.
122. The method of claim 121 wherein said protease is cathepsin B or cathepsin L.
123. A method of inhibiting microbial cell or viral growth or reproduction by inhibiting the enzymatic activity of cysteine proteases associated with such growth or reproduction, comprising contacting such protease with an inhibitory amount of a compound of claim 1 or 2.
124. The method of claim 123 wherein the cysteine protease is hepatitis A
virus 3C proteinase.
125. The method of claim 123 wherein the cysteine protease is hepatitis C
virus endopeptidase 2.
126. The method of claim 123 wherein the cysteine protease is picornain 3C
rhinovirus protease.
127. The method of claim 123 wherein the cysteine protease is foot and mouth disease virus L
proteinase.
128. The method of claim 123 wherein the cysteine protease is encephalomyelitis virus endopeptidase 2.
129. The method of claim 123 wherein the cysteine protease is picornain 2A
protease 130. A method of treating the symptoms associated with allergic response by inhibiting the enzymatic activity of cysteine proteases associated with such response, comprising contacting such protease with an inhibitory amount of a compound of claim 1 or 2.
131. The method of claim 130 wherein the protease is Der p I.
132. A method of treating the symptoms associated with a neurodegenerative disorder by inhibiting the enzymatic activity of cysteine proteases associated with such disease, comprising contacting such protease with an inhibitory amount of a compound of claim 1 or 2.
133. The method of claim 132 wherein the neurodegenerative disorder is Alzheimer's disease, Parkinson's disease or multiple sclerosis.
134. The method of claim 133 wherein said disorder is a result of ischemic-reperfusion injury.
135. The method of claim 134 wherein the ischemic-reperfusion injury is stroke.

136. The method of claim 134 wherein the ischemic-reperfusion injury is myocardial infarction, transplantation, vascular injury or cardiovascular collapse or shock.
137. A method of treating the symptoms associated with inflammatory and degenerative diseases by inhibiting the enzymatic activity of cysteine proteases associated with such diseases, comprising contacting such protease with an inhibitory amount of a compound of claim 1 or 2.
138. The method of claim 137 wherein the inflammatory disease is an arthridity.
139. The method of claim 138 wherein the arthridity is rheumatoid arthiritis or osteoarthritis.
140. The method of claim 137 wherein the inflammatory disease is periodontal disease.
141. The method of claim 107 wherein the compound is [2-[5-(3-methylbenzyl)-1,3,4-oxadiazolyl]carbonyl]-2-(S)-methylpropyl]-L-phenylalanamide-(3R)-(isobutyl)succinic acid.
142. The method of claim 107 wherein the compound is:
Acetyl-L-leucyl-N-[1-[2-[5-phenyl]-1,3,4-oxadiazolyl]carbonyl]-4-(guanidino)-butyl-L-leucyl amide;
Acetyl-L-leucyl-N-[1-[3-[5-methyl]-1,2,4-oxadiazolyl]carbonyl]-ethyl-L-leucyl amide;
Acetyl-L-leucyl-N-[1-[3-[5-methyl]-1,2,4-oxadiazolyl]carbonyl]-4-(guanidino)-butyl-L-leucyl amide;
Acetyl-L-tyrosinyl-L-valyl-N-[1-[2-[(5-phenyl)-1,3,4-oxadiazolyl]carbonyl]-2-carboxy-ethyl]-L-alanine amide; or Acetyl-L-Aspartyl-Valyl-N-[1-[2-[(5-phenyl)-1,3,4-oxadiazolyl] carbonyl]-2-(carboxy)-ethyl]-L-glutamyl amide.
143. The method of claim 107 wherein the compound is (t-butoxysuccinyl)-L-valyl-N-[1-[3-[5-(3-trifluoromethylbenzyl)-1,2,4-oxadiazolyl]carbonyl]-2-benzylidone]-L-prolinamide; or carboxysuccinyl-L-valyl-N-[1-[3-[5-(3-trifluoromethylbenzyl)-1,2, 4-oxadiazolyl]carbonyl)-2-benzylidone]-L-prolinamide.
144. The method of claim 103 wherein the compound is (benzyloxycarbonyl)-L-valyl-N-[1-(2-[5-(3-methylbenzyl)-1,3,4-oxadiazolyl]carbonyl)-2-(S)-methylpropyl)-L-prolinamide.
145. A method of detecting or quantifying the activity of a cysteine protease in a pure sample, mixture or a biological fluid or tissue, comprising contacting said protease with a compound of claim 1 or 2.
146. A method of purifying a cysteine protease in a sample, comprising contacting said protease with a compound of claim 1 or 2.