U.S. patent application number 11/490155 was filed with the patent office on 2006-12-28 for resistant-repellent retroviral protease inhibitors.
This patent application is currently assigned to Sequoia Pharmaceuticals, Inc.. Invention is credited to Michael Eissenstat, John W. Erickson, Sergei Gulnik, Abelardo Silva.
Application Number | 20060293286 11/490155 |
Document ID | / |
Family ID | 26994100 |
Filed Date | 2006-12-28 |
United States Patent
Application |
20060293286 |
Kind Code |
A1 |
Erickson; John W. ; et
al. |
December 28, 2006 |
Resistant-repellent retroviral protease inhibitors
Abstract
Resistance-repellent and multidrug resistant retroviral protease
inhibitors are provided. Pharmaceutical composition comprising such
compounds, and methods of using such compounds to treat HIV
infections in mammals, are also provided.
Inventors: |
Erickson; John W.;
(Frederick, MD) ; Eissenstat; Michael; (Frederick,
MD) ; Silva; Abelardo; (Columbia, MD) ;
Gulnik; Sergei; (Frederick, MD) |
Correspondence
Address: |
PROSKAUER ROSE LLP
1001 PENNSYLVANIA AVE, N.W.,
SUITE 400 SOUTH
WASHINGTON
DC
20004
US
|
Assignee: |
Sequoia Pharmaceuticals,
Inc.
Gaithersburg
MD
20879
|
Family ID: |
26994100 |
Appl. No.: |
11/490155 |
Filed: |
July 21, 2006 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
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10337349 |
Jan 7, 2003 |
7109230 |
|
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11490155 |
Jul 21, 2006 |
|
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60344788 |
Jan 7, 2002 |
|
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60383575 |
May 29, 2002 |
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Current U.S.
Class: |
514/109 ;
514/367; 514/375; 514/452; 548/152; 548/217; 549/362; 558/74 |
Current CPC
Class: |
Y02A 50/47 20180101;
C07D 495/04 20130101; G16B 15/00 20190201; C12N 9/506 20130101;
Y02A 90/26 20180101; A61K 31/337 20130101; Y02A 50/406 20180101;
G16C 20/50 20190201; A61P 31/12 20180101; C07D 491/04 20130101;
Y02A 50/471 20180101; C07D 275/03 20130101; Y02A 90/10 20180101;
C12N 9/88 20130101; C07D 493/04 20130101; A61P 31/18 20180101; Y02A
50/30 20180101; C07K 2299/00 20130101; C07D 307/20 20130101; G16B
20/00 20190201 |
Class at
Publication: |
514/109 ;
514/367; 514/375; 514/452; 548/152; 548/217; 549/362; 558/074 |
International
Class: |
C07F 9/02 20060101
C07F009/02; A61K 31/66 20060101 A61K031/66; C07D 277/62 20060101
C07D277/62; C07D 263/60 20060101 C07D263/60; C07D 319/14 20060101
C07D319/14; A61K 31/428 20060101 A61K031/428; A61K 31/423 20060101
A61K031/423 |
Claims
1-32. (canceled)
33. An HIV protease inhibitor represented by a formula: X-A-B-A'-X'
wherein X is a 5-7 membered non-aromatic monocyclic heterocycle,
wherein said heterocycle is optionally fused or bridged with one or
more 3-7 membered non-aromatic monocyclic heterocycle to form a
polycyclic system, wherein any of said heterocyclic ring systems
contains one or more heteroatoms selected from O, N, S, or P;
wherein any nitrogen forming part of the heterocycles may
optionally be substituted by R2, R3, R6, R7 or O; wherein any
sulfur may be optionally be substituted by one or two oxygen atoms;
wherein any P may be optionally be substituted by one or more of O
NR2, or S, and any of said ring systems optionally contains 1 to 6
substituents selected from the group consisting of R2, R3, R5, and
R6; A is ZCZNH, ZCOCONH, ZS(O).sub.2NH, ZP(O)(V)NH, CONH, COCONH,
S(O).sub.2NH, P(O)(V)NH, wherein Z is NR2, O, S, or C(R2).sub.2,
and V is OR2 or NR2; B is ##STR31## wherein D is selected from
alkyl, alkenyl, alkynyl, aryl, cycloalkyl, or aralkyl optionally
substituted with one or more groups selected from alkyl, halo,
nitro, cyano, CF.sub.3, C3-C7 cycloalkyl, C5-C7 cycloalkenyl, R6,
OR2, SR2, NHR2, OR3, SR3, NHR3, OR6, SR6, or NHR6; A' is N(D')E',
wherein D' is selected from alkyl, alkenyl, alkynyl, aryl,
cycloalkyl, or aralkyl optionally substituted by alkyl, halo,
nitro, cyano, CF.sub.3, O-alkyl, or S-alkyl, and E' is --CO-- or
--SO.sub.2--; X' is ##STR32## wherein G' and R' cannot both be H;
G' and R' are each independently: H or alkyl substituted by R3, R5,
R6 provided R5 is not halo; C2-C6 alkenyl, C2-C6 alkynyl, C3-C8
cycloalkyl, C5-C8 cycloalkenyl, and heterocyclo, which groups may
be optionally substituted with one or more substituents selected
from the group consisting of --OR2, C(O)N(R2).sub.2,
S(O).sub.nN(R2).sub.2, CN, SR2, SO.sub.nR2, COR2, CO.sub.2R2 or
NR2C(O)R2, R5, and R7; aryl or heteroaryl, wherein said aryl or
heteroaryl may be optionally substituted with one or more groups
selected from the group consisting of aryl, heteroaryl, R2, R3, R4,
and R6; C3-C7 cycloalkyl substituted by R2, R3, R5, R6; provided R2
is not H; CO.sub.2H or R7 provided R2 is not H or unsubstituted
alkyl; SO.sub.nN(R8).sub.2, SO.sub.nNR7R8, SR8, S(O).sub.nR8,
provided R8 is not H or methyl; and n is 1 or 2; and X'' is
selected from O or NR''; wherein R'' is H or alkyl optionally
substituted by R3, R5, R6; C2-C6 alkenyl, C2-C6 alkynyl, C3-C8
cycloalkyl, C5-C8 cycloalkenyl, and heterocyclo, which groups may
be optionally substituted with one or more substituents selected
from the group consisting of --OR2, C(O)N(R2).sub.2,
S(O).sub.nN(R2).sub.2, CN, SR2, SO.sub.nR2, COR2, CO.sub.2R2 or
NR2C(O)R2, R5, and R7; aryl or heteroaryl, wherein said aryl or
heteroaryl may be optionally substituted with one or more groups
selected from the group consisting of aryl, heteroaryl, R2, R3, R4,
and R6; C3-C7 cycloalkyl optionally substituted by R2, R3, R5, R6;
R7; NR3R3, NR6R6, NR7R7, NR3R6, NR6R7, NR3R7, NR2R3, NR2R6, NR2R7,
NR2R2; SO.sub.nN(R2).sub.2, SO.sub.nN(R3).sub.2,
SO.sub.nN(R6).sub.2, SO.sub.nN(R7).sub.2, SO.sub.nNR2R3,
SO.sub.nNR2R6, SO.sub.nNR2R7, SO.sub.nNR3R6, SO.sub.nNR3R7,
SO.sub.nNR6R7; S(O).sub.mR2, S(O).sub.mR3, S(O).sub.mR6, provided
R2 is not H; and m is 0, 1 or 2.
34. The compound according to claim 33, wherein X is ##STR33## Y is
O, or S; z is O, or S; and wherein any ring carbon is optionally
substituted by R2, R3, R5, or R6.
35. The compound according to claim 33, wherein X is ##STR34##
wherein G is C, O, or S; n is an integer between 1-2; and wherein
any ring carbon is optionally substituted by R2, R3, R5, or R6.
36. The compound according to claim 33, wherein X is ##STR35##
wherein J is independently CH.sub.2, or O, and wherein any ring
carbon is optionally substituted by R2, R3, R5, or R6.
37. The compound according to claim 33, wherein: X is ##STR36##
wherein any ring carbon is optionally substituted by R2, R3, R5, or
R6.
38. The compound according to claim 33, wherein X is ##STR37##
wherein each L is independently H, lower alkyl, oxo, or L forms a
carbocyclic or heterocyclic ring with M; each M is independently H,
OH, chloro, fluoro, or M forms a carbocyclic or heterocyclic ring
with Q, provided that if one M is OH, the other M is not OH; Q is
H, OH, amino, lower alkyl, alkylamino, alkoxy, halo, or forms a
3-7-membered carbocyclic or heterocyclic ring together with T; each
F is independently H, OH, lower alkyl, halo, or spirocylopropyl,
provided that if one R is OH, the other R is not OH; T is H or F,
or T forms a carbocyclic or heterocyclic ring together with F.
39. The HIV protease inhibitor according to claim 33, wherein X is
tetrahydrofurodihydrofuranyl, tetrahydrofurotetrahydrofuranyl,
tetrahydropyranotetrahydrofuranyl or
tetrahydropyranodihydrofuranyl; A is OCONH; B is ##STR38## wherein
D is aralkyl optionally substituted with one or more groups
selected from alkyl, halo, nitro, cyano, CF.sub.3, C3-C7
cycloalkyl, C5-C7 cycloalkenyl, R6, OR2, SR2, NHR2, OR3, SR3, NHR3,
OR6, SR6, and NHR6; and A' is N(D')E', wherein D' is alkyl,
alkenyl, alkynyl aryl, cycloalkyl, or aralkyl optionally
substituted by alkyl, halo, or CF.sub.3, and E' is
--SO.sub.2--.
40. The HIV protease inhibitor according to claim 33, wherein: X is
tetrahydrofurotetrahydrofuranyl; A is OCONH; B is ##STR39## wherein
D is benzyl; and A' is N(D')E', wherein D' is isobutyl and E' is
--SO.sub.2--;
41. The HIV protease inhibitor according to claim 33, wherein: X is
##STR40## wherein A3 is H, F or alkoxy; B3 is F, alkoxy, lower
alkyl, or A3 and B3 can form a 3-7 membered heterocyclic ring; Z'
is O, or S; and n is an integer between 1-3.
42. A compound according to claim 33, bound in a complex with wild
type or drug resistant mutant forms of HIV-1 protease.
43. A pharmaceutical composition comprising an effective amount of
an inhibitor according to claim 33 and a pharmaceutically
acceptable additive, excipient, or diluent.
44. A pharmaceutical composition comprising an effective amount
inhibitor according to claim 33 and another antiretroviral
agent.
45. A pharmaceutical composition comprising an effective amount of
an inhibitor according to claim 33 and a second HIV inhibitor.
46. A pharmaceutical composition comprising an inhibitor according
to claim 33 and an additional HIV protease inhibitor.
47. A pharmaceutical composition comprising an effective amount of
an inhibitor according to claim 33 and an HIV reverse transcriptase
inhibitor.
48. A method of treating a patient suffering from HIV infection,
comprising administering to said patient a composition according to
claim 33.
49. A method of treatment according to claim 33 wherein said
patient is suffering from a multi-drug resistant HIV infection.
50. An HIV protease inhibitor having the formula I: X-A-B-A'-X' I
wherein X is a moiety comprising first and second hydrogen bond
acceptor atoms H.sub.A1:X and H.sub.A2:X, wherein H.sub.A1:X forms
a hydrogen bond with N29 of HIV protease and H.sub.A2:X forms a
hydrogen bond with N30 of HIV protease at the relative positions
designated in Table 8; wherein A is an optionally substituted
linker moiety comprising a linear chain of 2-6 atoms, wherein A
comprises a hydrogen bond acceptor atom H.sub.A:A, and a hydrogen
bond donor atom H.sub.D:A, and wherein H.sub.A:A forms a hydrogen
bond with solvated water301 of said protease at a relative position
designated by O301, and HD:A forms a hydrogen bond with the
backbone CO atom of residue 27 of said protease at a relative
position designated by O27; wherein B comprises a hydrogen bond
donor or acceptor atom H.sub.D/A:B, wherein H.sub.D/A:B forms a
hydrogen bond with either or both carboxylate side chain oxygens of
Asp25 and Asp wherein B comprises a hydrogen bond donor or acceptor
atom H.sub.D/A:B, wherein H.sub.D/A:B forms a hydrogen bond with
either or both carboxylate side chain oxygens of Asp25 and Asp 125
of said protease at relative positions designated by OD1 25, OD2
25, OD1 125, and OD2 125; wherein A' is an optionally substituted
linker moiety comprising a linear chain of 2-6 atoms, comprising a
hydrogen bond acceptor atom H.sub.A:A', wherein H.sub.A:A' forms a
hydrogen bond with solvated water301 of said protease at a relative
position designated by O301; and wherein X' is a moiety comprising
a hydrogen bond acceptor atom H.sub.A:X', wherein H.sub.A:X' forms
a hydrogen bond with backbone NH atoms of residues 129 and/or 130
of said protease at relative positions designated by N129 and/or
N130.
51. A compound according to claim 50, bound in a complex with wild
type or drug resistant mutant forms of HIV-1 protease.
52. A pharmaceutical composition comprising an effective amount of
an inhibitor according to claim 50 and a pharmaceutically
acceptable additive, excipient, or diluent.
53. A pharmaceutical composition comprising an effective amount
inhibitor according to claim 50 and another antiretroviral
agent.
54. A pharmaceutical composition comprising an effective amount of
an inhibitor according to claim 50 and a second HIV inhibitor.
55. A pharmaceutical composition comprising an inhibitor according
to claim 50 and an additional HIV protease inhibitor.
56. A pharmaceutical composition comprising an effective amount of
an inhibitor according to claim 50 and an HIV reverse transcriptase
inhibitor.
57. A method of treating a patient suffering from HIV infection,
comprising administering to said patient a composition according to
claim 50.
58. A method of treatment according to claim 57 wherein said
patient is suffering from a multi-drug resistant HIV infection.
Description
[0001] This application is a divisional of non-provisional
application Ser. No. 10/337,349 filed on Jan. 7, 2003 which claims
priority to provisional application 60/383,575 filed on May 29,
2002 and 60/344,788 filed on Jan. 7, 2002, the contents of which
are herein incorporated by reference.
FIELD OF THE INVENTION
[0002] The present invention relates to retroviral protease
inhibitors and, more particularly, relates to novel compounds,
compositions and methods for inhibiting retroviral proteases. This
invention, in particular, relates to resistance-repellent HIV
protease inhibitors, compositions, and uses thereof for treating
HIV infections, particularly infections caused by one or more
species of drug resistant HIV strains.
BACKGROUND OF THE INVENTION
[0003] Acquired immune deficiency syndrome (AIDS) is a fatal
disease, reported cases of which have increased dramatically within
the past several years. Estimates of reported cases in the very
near future also continue to rise dramatically. Consequently, there
is a great need to develop drugs and vaccines to combat AIDS.
[0004] The AIDS virus was first identified in 1983. It has been
known by several names and acronyms. It is the third known
T-lymphocyte virus (HTLV-III), and it has the capacity to replicate
within cells of the immune system, causing profound cell
destruction. The AIDS virus is a retrovirus, a virus that uses
reverse transcriptase during replication. This particular
retrovirus is also known as lymphadenopathy-associated virus (LAV),
AIDS-related virus (ARV) and, most recently, as human
immunodeficiency virus (HIV). Two distinct families of HIV have
been described to date, namely HIV-1 and HIV-2. The acronym HIV is
used hereinafter to refer to HIV viruses generically.
[0005] Specifically, HIV is known to exert a profound cytopathic
effect on CD4+ helper/inducer T-cells, thereby severely
compromising the immune system. HIV infection also results in
neurological deterioration and, ultimately, in the death of the
infected individual.
[0006] The field of viral chemotherapeutics has developed in
response to the need for agents effective against retroviruses, in
particular HIV. Theoretically, there are many ways in which an
agent can exhibit anti-retroviral activity. The HIV genome encodes
several viral-specific enzymes, such as reverse transcriptase (RT),
integrase and protease (PR); viral-specific regulatory proteins,
such as tat, rev, nef and vif; and, numerous viral-specific
structural proteins, and numerous viral-specific structural
proteins, such as capsid, nucleocapsid, matrix, and envelope
proteins. Many of these proteins are essential for viral
replication. Accordingly, viral replication theoretically could be
inhibited through inhibition of any one or all of the proteins
involved in viral replication. In practice, however, only
inhibitors of RT and PR are currently available for antiviral
therapy.
[0007] Nucleoside analogues (NRTIs), such as
3'-azido-2',3'-dideoxythymidine (AZT), 2',3'-dideoxycytidine (ddC),
and 2',3'-dideoxyinosine (ddI) are known to inhibit HIV RT. There
also exist non-nucleoside inhibitors (NNRTIs) specific for HIV-1
RT, such as Nevirapine, and Efavirenz.
[0008] Retroviral PR inhibitors (PIs) have also been identified as
a class of anti-retroviral agents. The retroviral PR processes
polyprotein precursors into viral structural proteins and
replicative enzymes. This processing is essential for the assembly
and maturation of fully infectious virions. Accordingly, the design
of PIs that selectively inhibit PR has been an important
therapeutic goal in the treatment of HIV infections and AIDS.
Strategies used in the design of HIV PIs include substrate-based,
peptidomimetic, transition state-based, and structure-based drug
design (Wlodawer & Erickson, Ann. Rev. Biochem., 62, 543-585
(1992)).
[0009] Numerous classes of potent peptidic inhibitors of PR have
been designed using the natural cleavage site of the precursor
polyproteins as a starting point. These inhibitors typically are
peptide substrate analogs in which the scissile P1-P1' amide bond
has been replaced by a non-hydrolyzable isostere with tetrahedral
geometry (Moore et al., Perspect. Drug Dis. Design, 1, 85 (1993);
Tomasselli et al., Int. J. Chem. Biotechnology, 6 (1991); Huff, J.
Med. Chem., 34, 2305 (1991); Norbeck et al., Ann. Reports Med.
Chem., 26, 141 (1991); Meek, J. Enzyme Inhibition, 6, 65
(1992)).
[0010] The design of HIV-1 PIs based on the transition-state
mimetic concept has led to the generation of a variety of peptide
derivatives highly active against viral replication in vitro
(Erickson et al., Science; 249, 527-533 (1990); Kramer et al.,
Science, 231, 1580-1584 (1986); McQuade et al., Science, 247,
454-456 (1990); Meek et al., Nature (London), 343, 90-92 (1990);
Roberts et al., Science, 248, 358-361 (1990)). These active agents
contain a non-hydrolyzable, dipeptide isostere such as
hydroxyethylene (McQuade et al., supra; Meek et al., Nature
(London), 343, 90-92 (1990); Vacca et al., J. Med. Chem., 34,
1225-1228 (1991)) or hydroxyethylamine (Rich et al., J. Med. Chem.,
33, 1285-1288 (1990); Roberts et al., Science, 248, 358-361 (1990))
as an active moiety which mimics the putative transition state of
the aspartic protease-catalyzed reaction.
[0011] Two-fold (C2) symmetric inhibitors of HIV protease represent
another class of potent HIV PIs which were created by Erickson et
al. on the basis of the three-dimensional symmetry of the enzyme
active site (Erickson et al., supra).
[0012] Typically, the usefulness of currently available HIV PIs in
the treatment of AIDS has been limited by relatively short plasma
half-life, poor oral bioavailability, and the technical difficulty
of scale-up synthesis (Meek et al. (1992), supra). Although these
inhibitors are effective in preventing the retroviral PR from
functioning, the inhibitors suffer from some distinct
disadvantages. Generally, peptidomimetics make poor drugs due to
their potential adverse pharmacological properties, i.e., poor oral
absorption, poor stability and rapid metabolism (Plattner et al.,
Drug Discovery Technologies, Clark et al., eds., Ellish Horwood,
Chichester, England (1990)). Furthermore, since the active site of
the PR is hindered, i.e., has reduced accessibility as compared to
the remainder of the PR, the ability of the inhibitors to access
and bind in the active site of the PR is impaired. Those inhibitors
that do bind are generally poorly water-soluble, causing distinct
problems for formulation and drug delivery.
[0013] There are currently six FDA-approved PIs for clinical
use--Saquinavir, Ritonavir, Indinavir, Nelfinavir, Amprenavir and
Lopinavir. When used alone or in combination with RT inhibitors,
PIs dramatically suppress viral replication in HIV-infected
individuals. Accordingly, PIs have become "first-line" antiviral
agents for the control of HIV-1 (HIV) infections and are widely
used in most highly active anti-retroviral therapy (HAART) regimens
(Boden & Markowitz, Antimicrob. Agents Chemo., 42, 2775-2783,
(1998)). Despite their success, the widespread use of PIs has led
to the emergence of several thousands of genetically distinct, drug
resistant HIV variants, many of which are cross-resistant to the
PIs as a class (Richman, Adv. Exp. Med. Biol., 392, 383-395 (1996);
Boden & Markowitz (1998), supra; Shafer et al. Ann. Intern.
Med., 128, 906-911(1998)).
[0014] The ability of HAART to provide effective long-term
antiretroviral therapy for HIV-1 infection has become a complex
issue since 40 to 50% of those who initially achieve favorable
viral suppression to undetectable levels experience treatment
failure (Grabar et al., AIDS, 14, 141-149 (1999); Wit et al., J.
Infect. Dis., 179, 790-798 (1999)). Moreover, 10 to 40% of
antiviral therapy-naive individuals infected with HIV-1 have
persistent viral replication (plasma HIV RNA>500 copies/ml)
under HAART (Gulick et al., N. Engl. J. Med., 337, 734-739 (1997);
Staszewski et al., N. Engl. J. Med., 341, 1865-1873 (1999)),
possibly due to transmission of drug-resistant HIV-1 variants
(Wainberg and Friedland, JAMA, 279, 1977-1983 (1998)). In addition,
it is evident that with these anti-HIV drugs only partial
immunologic reconstitution is attained in patients with advanced
HIV-1 infection.
[0015] The clinical manifestations of drug resistance are viral RNA
rebound and decreased CD4 cell-counts in the continued presence of
drug. The majority of clinical resistance cases are due to viral
adaptation through the generation and selection of mutations in the
PR and RT genes. Mutant viruses can be generated through errors in
reverse transcription of viral RNA, viral RNA synthesis, and
recombination events (Coffin, Retroviruses pp. 143-144, Cold Spring
Harbor Laboratory Press, Plainview (1997)). Mutations within the
protease gene that confer clinical drug resistance have emerged for
all of the FDA-approved HIV PR inhibitors. The rapid development of
drug resistance to PIs, combined with the transmissibility of
drug-resistant HIV strains to newly-infected individuals, has
resulted in the emergence of a new epidemic of multi-drug resistant
AIDS (mdrAIDS). Multi-drug resistant AIDS is caused by a complex
spectrum of genetically distinct, infectious new HIV strains that
resist most or all forms of currently available treatment.
[0016] Accordingly, drug resistant HIV strains represent distinct
infectious entities from a therapeutic viewpoint, and pose new
challenges for drug design as well as drug treatment of existing
infections. Substitutions have been documented in over 45 of the 99
amino acids of the HIV protease monomer in response to protease
inhibitor treatment (Mellors, et al., International Antiviral News,
3, 8-13(1995); Eastman, et al., J. Virol., 72, 5154-5164(1998);
Kozal, et al., Nat. Med., 2, 753-759(1996)). The particular
sequence and pattern of mutations selected by PIs is believed to be
somewhat drug-specific and often patient-specific, but high level
resistance is typified by multiple mutations in the protease gene
which give rise to cross-resistance to all of the PIs.
[0017] The challenge of tackling drug resistance is perhaps best
illustrated by considering the dynamics of a typical HIV infection.
Approximately 10.sup.12 virions are produced in an HIV infected
individual every day. The mutation rate of HIV is approximately 1
per genome, which numbers 10.sup.4 nucleotide bases. Therefore,
every nucleotide in the genome is mutated 10.sup.8 times per round
of replication in the patient. This means that all possible single
site mutations are present in at least the 0.01% level. Because of
this, drugs that can be rendered ineffective with a single mutation
from wild type have the shortest effective lifetime in monotherapy
settings. The apparently large number of possible mutational
pathways, possible mutational combinations, and the danger of
generating class-specific cross resistance can make the choice of a
subsequent protease inhibitor-containing combination regimen for
"salvage therapy" seem very complicated and risky. Even the choice
of protease inhibitor with which to initiate therapy, so-called
"first-line" therapy, can be a risky enterprise that may
inadvertently select for an undesired resistance pathway.
Drug-naive HIV-infected individuals pose even more of a risk for
developing resistance to first-line therapies.
[0018] For the reasons outlined above, the development of new
anti-HIV-1 therapeutics presents formidable challenges different
from those in the design of the first line drugs, particularly in
regard to consideration of selection pressure mechanisms in
addition to the conventional issues of potency, pharmacology,
safety, and mechanism of drug action. Indeed, HIV-1 can apparently
develop resistance to any existing anti-HIV-1 therapeutic. In
particular, the very features that contribute to the specificity
and efficacy of RTIs and PIs provide the virus with a strategy to
mount resistance (Erickson and Burt, Annu. Rev. Pharmacol.
Toxicol., 36, 545-571 (1996); Mitsuya and Erickson, Textbook of
AIDS Medicine, pp. 751-780, Williams and Wilkins, Baltimore
(1999)), and it seems highly likely that this resistance issue will
remain problematic for years to come.
[0019] Despite numerous studies of drug resistance to PIs,
successful strategies to design inhibitors directly targeted
against drug resistant HIV have been lacking. Instead, efforts have
been directed at identifying drugs with increased potency to wild
type virus, and with longer pharmacological half-lives (exemplified
by Amprenavir). Another approach has been to develop PIs that are
sensitive to pharmacologic "boosting" using Ritonavir, a PI that is
also a potent inhibitor of the cytochrome enzymes. The latter
approach, exemplified by Kaletra (a Lopinavir/Ritonavir
combination), involves higher total drug exposures to PIs which,
over time, may lead to long term, serious side effects. Several
other PIs have been identified based on efforts to improve plasma
half-life and bioavailability. For example, PIs incorporating the
2,5-diamino-3,4-disubstituted-1,6-diphenylhexane isostere are
described in Ghosh et. al., Bioorg. Med. Chem. Lett., 8, 687-690
(1998) and U.S. Pat. No. 5,728,718 (Randad et al.), both of which
are incorporated herein by reference in their entirety. HIV PIs,
which incorporate the hydroxyethylamine isostere, are described in
U.S. Pat. No. 5,502,060 (Thompson et al.), U.S. Pat. No. 5,703,076
(Talley et al.), and U.S. Pat. No. 5,475,027 (Talley et al.).
[0020] Recent studies have revealed the structural and biochemical
mechanisms by which mutations in the PR gene of HIV confer drug
resistance in the presence of PIs. An important conclusion that
emerges from the body of evidence on resistance to PIs is that HIV
variants that exhibit cross-resistance to first-line PIs should be
considered to be unique infectious agents. New therapeutic agents
need to be developed to successfully treat patients infected with
these viruses. New strategies for drug discovery need to be
explored to develop effective protease inhibitor-based treatments
for patients with multidrug resistant virus. HIV protease is one
the most intensively studied molecular targets in the history of
infectious disease.
[0021] More recently, new mutant strains of HIV have emerged that
are resistant to multiple, structurally diverse, experimental and
chemotherapeutic HIV PIs. Such mdrHIV strains are typically found
in infected patients who have undergone treatment with a
combination of PIs or with a series of different PIs. The number of
reported cases of patients infected with mdrHIV is rising steadily.
Tragically for these patients, the available options for AIDS
chemotherapy and/or HIV management is severely limited or is,
otherwise, completely nonexistent.
[0022] A biochemical fitness profiling strategy has recently been
used to identify a novel subclass of potent PIs that have
broad-based activity against mdrHIV (Gulnik et al., (1995) supra;
Erickson et al., WO 99/67254; Erickson et al., WO 99/67417).
[0023] In view of the foregoing problems, there exists a need for
inhibitors against drug resistant and mdrHIV strains. Further,
there exists a need for inhibitors against drug resistant and
multi-drug resistant HIV proteases (mdrPR). Further still, there
exists a need for inhibitors of HIV that can prevent or slow the
emergence of drug resistant and mdrHIV strains in infected
individuals.
[0024] Inhibitors with the ability to inhibit mdrHIV strains, and
to slow the emergence of drug resistant strains in wild type HIV
infections, are defined as "resistance-repellent" inhibitors. There
also exists a need for robust methods that can be used to design
"resistance-repellent" inhibitors.
SUMMARY OF THE INVENTION
[0025] The present invention provides such resistance-repellent
inhibitors of mdrPR, their compositions, methods of design, and
uses thereof for treating mdrHIV and wtHIV infections in salvage
therapy and first-line therapy modalities.
[0026] More particularly, the invention provides HIV protease
inhibitors represented by the formula I: X-A-B-A'-X' I
[0027] where X is a moiety that contains two or more hydrogen bond
acceptors capable of interacting with the backbone NH atoms of
residues 29 and 30 of an HIV protease, A is a 2-6 atom linker that
contains at least one hydrogen bond acceptor that interacts with
the flap water, and one hydrogen bond donor that interacts with the
backbone CO atom of residue 27, B contains 1-3 atoms that can form
hydrogen bonds with either or both carboxylate side chain oxygens
of Asp25 and Asp 125 of said protease, A' is a 2-6 atom linker that
contains at least one hydrogen bond acceptor that interacts with
the flap water; and X' is a moiety that can form one or more
hydrogen bonds with the backbone NH atoms of residues 129 and/or
130, provided that the compound of Formula I is not any of the
compounds described in J. Med. Chem. 39:3278-3290 (1996), in
Bioorg. Med. Chem. Lett. 8:687-690 (1998), or Bioorg. Med. Chem.
Lett. 8:979-982 (1998).
[0028] The invention also provides a compound as described above,
bound in a complex with wild type or drug resistant mutant forms of
HIV-1 protease.
[0029] The invention further provides pharmaceutical compositions,
comprising an inhibitor as described above, together with a
pharmaceutically acceptable additive, excipient, or diluent. The
composition may further comprise an additional HIV protease
inhibitor and/or an HIV reverse transcriptase inhibitor.
[0030] The invention further provides methods of treating a patient
suffering from HIV infection, comprising administering to the
patient a pharmaceutical composition as described above.
BRIEF DESCRIPTION OF THE DRAWINGS
[0031] FIG. 1 shows the structure of 1.
[0032] FIG. 2 shows in vitro selection of HIV-1 variants resistant
to 1 and amprenavir. A laboratory HIV-1 strain, HIV-1.sub.NL4-3,
was passaged in the presence of increasing concentrations of 1
(.largecircle.) or amprenavir (.circle-solid.) in MT-2 cells. The
selection was carried out in a cell-free manner for a total of
34-64 passages with drug concentrations escalating from 0.0005 to
10 .mu.M. Nucleotide sequences of proviral DNA were determined
using cell lysates of HIV-1-infected MT-2 cells at the termination
of each indicated passage.
[0033] FIG. 3 shows sequence analysis of the protease-encoding
region of HIV-1 passaged in the presence of 1. The amino acid
sequences of protease deduced from nucleotide sequences of the
protease-encoding region of HIV-1 clones determined at nine
different passages are illustrated. The fraction of clones examined
is indicated on the right. The amino acid sequence of protease of a
wild-type pNL4-3 clone is shown as a reference. Identity with this
sequence at individual amino acid positions is indicated by
dots.
[0034] FIG. 4 shows a backbone diagram of the dimeric HIV-1
protease. A model of 1 bound in the active site is shown in stick
lines. The six residues which are commonly mutated during in vitro
selection with 1 are indicated by spheres. Two of these residues
lie within the active site (residue 28 and 50), while the other
four residues lie outside of the active site (residue 10, 46, 71
and 88).
[0035] FIG. 5 shows modeling of 1 bound in the active site of HIV-1
protease. Hydrogen bonds are represented as dotted lines.
[0036] FIG. 6 shows the structures of some compounds of general
formula I.
[0037] FIG. 7 shows a set of three-dimensionally-conserved
substructures of an HIV protease substrate binding site and the
substructure of atoms of an inhibitor interacting with the
conserved substructure of the protease.
[0038] Table 1 shows the sensitivities of three HIV strains to
various HIV drugs.
[0039] Table 2 shows the PI sensitivities of HIV strains isolated
from heavily-drug experienced individuals.
[0040] Table 3 shows amino acid substitutions in PR and
sensitivities of drug-resistant HIV-1 strains to protease
inhibitors.
DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENTS
[0041] The invention provides `resistance-repellent` retroviral
protease inhibitors. A `resistance-repellent` protease inhibitor
("PI") is a compound that retains inhibitory activity, or potency,
over a broad spectrum of related but non-identical retroviral
proteases. Examples of resistance-repellent PIs include, but are
not limited to, PIs that inhibit wild type HIV-1 protease derived
from any clade B virus and 1) a wild type retroviral protease from
one or more different retroviruses, such as HIV-2 protease; or 2)
mutant HIV-1 proteases with single active site mutations at
residues 30, 82 and 84; or 3) mutant HIV-1 proteases with single
active site mutations at residues 47, 48, and 50; or 4) mutant
HIV-1 proteases with double active site mutations at residues 82
and 84; or 5) mutant HIV-1 proteases with double active site
mutations at residues 47 and 48, 47 and 50, or 48 and 50; or 6)
mutant HIV-1 proteases with double active site mutations at
residues 48 and 82, 48 and 90, or 82 and 90; or 7) mutant HIV-1
proteases with three or more active site mutations in any
combination at residues 32, 47, 48, 50, 82, 84 or 90.
[0042] The term "pharmaceutically effective amount" refers to an
amount effective in treating a virus infection, for example an HIV
infection, in a patient either as monotherapy or in combination
with other agents. The term "treating" as used herein refers to the
alleviation of symptoms of a particular disorder in a patient or
the improvement of an ascertainable measurement associated with a
particular disorder. The term "prophylactically effective amount"
refers to an amount effective in preventing a virus infection, for
example an HIV infection, in a patient. As used herein, the term
"patient" refers to a mammal, including a human.
[0043] The applicants have found that compounds having the general
formula I are effective against a wide variety of PI-resistant HIV
strains X-A-B-A'-X' I
[0044] where X is a moiety that contains two or more hydrogen bond
acceptors capable of interacting with the backbone NH atoms of
residues 29 and 30 of an HIV protease, A is a 2-6 atom linker that
contains at least one hydrogen bond acceptor that interacts with
the flap water, and one hydrogen bond donor that interacts with the
backbone CO atom of residue 27, B contains 1-3 atoms that can form
hydrogen bonds with either or both carboxylate side chain oxygens
of Asp25 and Asp 125 of said protease, A' is a 2-6 atom linker that
contains at least one hydrogen bond acceptor that interacts with
the flap water; and X' is a moiety that can form one or more
hydrogen bonds with the backbone NH atoms of residues 129 and/or
130. Some compounds conforming to this general formula have been
described and the present invention specifically excludes those
compounds.
[0045] Resistance-repellent PIs should generally also retain
inhibitory activity, or potency, over a broad spectrum of related
but non-identical retroviruses. In particular, resistance-repellent
PIs should inhibit all HIV-1 virus strains that contain a gene
sequence of the protease region of the HIV-1 pol gene that is
typified by one or more `wild type` strains derived from clade B
and: 1) HIV-1 virus strains that contain a gene sequence of the
protease region of the HIV-1 pol gene derived from wild type,
non-clade B viruses; or 2) wild type HIV-2 virus strains; or 3)
HIV-1 virus strains derived from patients who are infected with
HIV-1 that contain mutations in the protease gene.
[0046] Comparative analysis of the x-ray crystal structures of
complexes of different inhibitors bound to wild type and mutant
forms of HIV protease has led the applicants to the insight that a
substructure in the active site of HIV protease is
structurally-conserved. It has also been discovered that
compositions that form selective interactions with this conserved
substructure, have attributes of resistance-repellent inhibitors
HIV protease. This insight has not been previously described. These
insights have led the applicants to design improved HIV PI
compounds that are effective against multidrug resistant HIV
strains.
[0047] In a preferred embodiment, the instant invention provides an
HIV protease inhibitor represented by a formula: X-A-B-A'-X'
[0048] wherein,
[0049] X is a moiety that contains two or more hydrogen bond
acceptors capable of interacting with the backbone NH atoms of
residues 29 and 30 of said protease;
[0050] A is a 2-6 atom linker that contains at least one hydrogen
bond acceptor that interacts with the flap water, and one hydrogen
bond donor that interacts with the backbone CO atom of residue 27
of said protease;
[0051] B contains 1-3 atoms that can form hydrogen bonds with
either or both carboxylate side chain oxygens of Asp25 and Asp 125
of said protease;
[0052] A' is a 2-6 atom linker that contains at least one hydrogen
bond acceptor that interacts with a flap water of said
protease;
[0053] X' is a moiety that can form one or more hydrogen bonds with
the backbone NH atoms of residues 129 and/or 130 of said
protease.
[0054] In a particular embodiment the invention provides an HIV
protease inhibitor represented by the formula I: X-A-B-A'-X' I
[0055] wherein X is a moiety that contains two or more hydrogen
bond acceptors capable of interacting with the backbone NH atoms of
residues 29 and 30 of an HIV protease;
[0056] A is a 2-6 atom linker that contains at least one hydrogen
bond acceptor that interacts with a flap water of said protease,
and one hydrogen bond donor that interacts with the backbone CO
atom of residue 27 of said proteease;
[0057] B contains 1-3 atoms that can form hydrogen bonds with
either or both carboxylate side chain oxygens of Asp25 and Asp 125
of said protease;
[0058] A' is a 2-6 atom linker that contains at least one hydrogen
bond acceptor that interacts with the flap water of said protease;
and
[0059] X' is a moiety that can form one or more hydrogen bonds with
the backbone NH atoms of residues 129 and/or 130 of said protease;
provided that the compound of Formula I is not any of the compounds
described in J. Med. Chem. 39:3278-3290 (1996), in Bioorg. Med.
Chem. Lett. 8:687-690 (1998), or Bioorg. Med. Chem. Lett. 8:979-982
(1998).
[0060] In another embodiment, the invention provides an HIV
protease inhibitor represented by a formula: X-A-B-A'-X'
[0061] wherein:
[0062] X is independently a 5-7 membered non-aromatic monocyclic
heterocycle, wherein said heterocycle is optionally fused with 1 or
2 3-7 membered non-aromatic monocyclic heterocycles, wherein said
5-7 membered non-aromatic monocyclic heterocycle is substituted by
at least a group R4 on a carbon of said heterocycle adjacent to a
heteroatom wherein R4 may optionally be part of the fused
heterocycles; and wherein any of said heterocyclic ring systems has
one or more heteroatoms selected from N, O, and S, wherein N is
optionally substituted by R2 and S is optionally substituted by one
or two oxygen atoms, and wherein any of said ring systems is
optionally substituted 1 to 6 times by R5;
[0063] A is ZCONH, ZCOCONH, ZS(O).sub.2NH, ZP(O)(V)NH, CONH,
COCONH, S(O).sub.2NH, P(O)(V)NH, wherein Z is O, NR2, C(R2).sub.2,
and V is OR2, NR2;
[0064] B is ##STR1## wherein D is selected from C1-C6 alkyl, C2-C4
alkenyl optionally substituted with one or more groups selected
from C3-C7 cycloalkyl, C5-C7 cycloalkenyl, OR2, SR2, NHR2, OR3,
SR3, NHR3, OR6, SR6, or NHR6;
[0065] A' is N(D')E', wherein D' is selected from C1-C15 alkyl,
C2-C15 alkenyl or C2-C15 alkynyl, and E' is --CO-- or
--SO.sub.2--;
[0066] X' is selected from the group consisting of R2, R3, and R6,
provided that when X' is H, E' is not --SO.sub.2--;
[0067] R2 is H or C1-C6 alkyl optionally substituted by R3, R5, or
R6,
[0068] R3 is C2-C6 alkenyl, C2-C6 alkynyl, C3-C8 cycloalkyl, C5-C8
cycloalkenyl, or heterocyclo, which groups may be optionally
substituted with one or more substituents selected from the group
consisting of --OR2, C(O)N(R2).sub.2, S(O).sub.nN(R2).sub.2, CN,
SR2, SO.sub.nR2, COR2, CO.sub.2R2 or NR2C(O)R2, R5, and R7;
[0069] R4 is N(R8).sub.2, NHOH, N(R8)COR8, NR8S(O).sub.nR8,
NR8C[.dbd.N(R8)]N(R8).sub.2, N(R8)N(R8)C(O)R8,
NR8PO.sub.nN(R8).sub.2, NR8PO.sub.nOR8, OH, OR8, OC(O)R8, OC(S)R8,
OC(O)N(R8).sub.2, OC(S)N(R8).sub.2, OPO.sub.n(R8).sub.2, R2OH,
R2-halo, CN, COR8, CO.sub.2R8, CON(R8).sub.2, C(O)N(R8)N(R8).sub.2,
S(O).sub.nR8, SO.sub.2N(R8).sub.2, halo, NO.sub.2, or SR8;
[0070] R5 is OH, OR8, N(R8).sub.2, NHOH, N(R8)COR8,
NR8S(O).sub.nR8, NR8C[.dbd.N(R8)]N(R8).sub.2, N(R8)N(R8)C(O)R8,
NR8PO.sub.nN(R8).sub.2, NR8PO.sub.nOR8, R2OH, R2-halo, CN, COR8,
CO.sub.2R8, CON(R8).sub.2, C(O)N(R8)N(R8).sub.2, S(O).sub.nR8,
SO.sub.2N(R8).sub.2, halo, NO.sub.2, SR8, oxo, .dbd.N--OH,
.dbd.N--OR8, .dbd.N--N(R8).sub.2, .dbd.NR8,
.dbd.NNR8C(O)N(R8).sub.2, .dbd.NNR8C(O)OR8,
.dbd.NNR8S(O).sub.nN(R8).sub.2, or .dbd.NNR8S(O).sub.n(R8),
.dbd.NNR8C(O)R8,
[0071] or R5 is C2-C6 alkenyl, C2-C6 alkynyl, C3-C8 cycloalkyl,
C5-C8 cycloalkenyl, or heterocyclo, which groups may be optionally
substituted with one or more substituents selected from the group
consisting of --OR2, C(O)NR2, S(O).sub.nN(R2).sub.2, CN, SR2,
SO.sub.nR2, COR2, CO.sub.2R2 or NR2C(O)R2, R5, and R7,
[0072] or R5 is C(O)R2, C(O)R3, C(O)R6, C(S)R2, C(S)R3, C(S)R6,
C(Z)N(R2).sub.2, C(Z)N(R3).sub.2, C(Z)N(R6).sub.2, C(Z)NR2R3,
C(Z)NR2R6, C(Z)NR3R6, CO.sub.2R2; provided R2 is not H; CO.sub.2R3,
or CO.sub.2R6;
[0073] R6 is aryl or heteroaryl, wherein said aryl or heteroaryl
may be optionally substituted with one or more groups selected from
the group consisting of aryl, heteroaryl, R2, R3, and R4;
[0074] R7 is C(O)R2, C(O)R3, C(O)R6, C(S)R2, C(S)R3, C(S)R6,
C(Z)N(R2).sub.2, C(Z)N(R3).sub.2, C(Z)N(R6).sub.2, C(Z)NR2R3,
C(Z)NR2R6, C(Z)NR3R6, or CO.sub.2R2; provided R2 is not H;
CO.sub.2R3, or CO.sub.2R6
[0075] R8 is H or C1-C6 alkyl optionally substituted by R3, R5, or
R6,
[0076] or R8 is C2-C6 alkenyl, C2-C6 alkynyl, C3-C8 cycloalkyl,
C5-C8 cycloalkenyl, or heterocyclo, which groups may be optionally
substituted with one or more substituents selected from the group
consisting of --OR2, C(O)NR2, S(O).sub.nN(R2).sub.2, CN, SR2,
SO.sub.nR2, COR2, CO.sub.2R2 or NR2C(O)R2, R5, and R7,
[0077] or R8 is aryl or heteroaryl, wherein said aryl or heteroaryl
may be optionally substituted with one or more groups selected from
the group consisting of aryl, heteroaryl, R2, R3, R4, and R6;
[0078] Z is O, S;
[0079] each n is independently an integer between 1-2; its
stereoisomeric forms; and its pharmacologically acceptable
salts.
[0080] Preferably, X is ##STR2##
[0081] wherein
[0082] Y is O, NH, or S;
[0083] Z is O, NH, or S; and
[0084] wherein any ring carbon is optionally substituted by R2, R3,
R5, R6.
[0085] Preferably X is ##STR3##
[0086] wherein
[0087] G is C, O, NR.sub.2, or S;
[0088] n is an integer between 1-2; and
[0089] wherein any ring carbon is optionally substituted by R2, R3,
R5, R6.
[0090] Preferably, X is ##STR4##
[0091] wherein
[0092] J is independently CH2, or O, or J is a bond; and
[0093] wherein any ring carbon is optionally substituted by R2, R3,
R5, R6.
[0094] Preferably, X is ##STR5##
[0095] wherein any ring carbon is optionally substituted by R2, R3,
R5, or R6.
[0096] Preferably, X is ##STR6##
[0097] wherein
[0098] each L is independently H, lower alkyl, oxo, or L forms a
carbocyclic or heterocyclic ring with M;
[0099] each M is independently H, OH, chloro, fluoro, or M forms a
carbocyclic or heterocyclic ring with Q, provided that if one M is
OH, the other M is not OH;
[0100] Q is H, OH, amino, lower alkyl, alkylamino, alkoxy, halo, or
forms a 3-7-membered carbocyclic or heterocyclic ring together with
T;
[0101] each R is independently H, OH, lower alkyl, halo, or
spirocylopropyl, provided that if one R is OH, the other R is not
OH;
[0102] T is H or F, or T forms a carbocyclic or heterocyclic ring
together with C;
[0103] In another preferred embodiment, the invention also provides
an HIV protease inhibitor represented by a formula: X-A-B-A'-X'
[0104] wherein:
[0105] X is a 5-7 membered non-aromatic monocyclic heterocycle,
wherein said heterocycle is fused with at least one 3-7 membered
non-aromatic monocyclic heterocycle to form a polycyclic system,
preferably bicyclic, wherein at least one carbon atom is
substituted by two heteroatoms; and wherein any of said
heterocyclic ring systems contains one or more heteroatoms selected
from O, N, S; wherein any nitrogen forming part of the heterocycles
may optionally be substituted by R2, R3, R6, R7 or O; wherein any
sulfur may be optionally be substituted by one or two oxygen atoms;
and any of said ring systems optionally contains 1 to 6
substituents selected from the group consisting of R2, R3, R5, and
R6;
[0106] A is ZCZNH; wherein Z is independently NR2, O, or S;
[0107] B is ##STR7## wherein D is alkyl, alkenyl, alkynyl, aryl,
cycloalkyl, or aralkyl optionally substituted by alkyl, halo,
nitro, cyano, CF3, O -alkyl or S-alkyl;
[0108] A' is N(D')E', wherein D' is alkyl, alkenyl, alkynyl aryl,
cycloalkyl, or aralkyl optionally substituted by alkyl, halo,
CF.sub.3, and E' is SO.sub.2;
[0109] X' is selected from the group consisting of aryl and
heteroaryl, which are substituted with one or more of the following
groups:
[0110] OR3, OR6, OR7, OR2 provided R2 is not H or unsubstituted
alkyl;
[0111] alkyl substituted by R3, R5, R6 provided R5 is not halo;
[0112] 2-C6 alkenyl, C2-C6 alkynyl, C3-C8 cycloalkyl, C5-C8
cycloalkenyl, and heterocyclo, which groups may be optionally
substituted with one or more substituents selected from the group
consisting of --OR2, C(O)N(R2).sub.2, S(O).sub.nN(R2).sub.2, CN,
SR2, SO.sub.nR2, COR2, CO.sub.2R2 or NR2C(O)R2, R5, and R7;
[0113] aryl or heteroaryl, wherein said aryl or heteroaryl may be
optionally substituted with one or more groups selected from the
group consisting of aryl, heteroaryl, R2, R3, R4, and R6;
[0114] C3-C7 cycloalkyl substituted by R2, R3, R5, R6; provided R2
is not H;
[0115] CO.sub.2H, R7 provided Z is N, O, S and provided R2 is not H
or unsubstituted alkyl;
[0116] NR3R3, NR6R6, NR7R7, NR3R6, NR6R7, NR3R7, NR2R3, NR2R6,
NR2R7, NR2R2 provided R2 is not H or unsubstituted alkyl;
[0117] SO.sub.nN(R2).sub.2, SO.sub.nN(R3).sub.2,
SO.sub.nN(R6).sub.2, SO.sub.nN(R7).sub.2, SO.sub.nNR2R3,
SO.sub.nNR2R6, SO.sub.nNR2R7, SO.sub.nNR3R6, SO.sub.nNR3R7,
SO.sub.nNR6R7, wherein n=1 or 2;
[0118] S(O).sub.nR2, S(O).sub.nR3, S(O).sub.nR6, provided R2 is not
H or methyl; and n is 0, 1 or 2;
[0119] R2 is H or C1-C6 alkyl optionally substituted by R3, R5, or
R6,
[0120] R3 is C2-C6 alkenyl, C2-C6 alkynyl, C3-C8 cycloalkyl, C5-C8
cycloalkenyl, or heterocyclo, which groups may be optionally
substituted with one or more substituents selected from the group
consisting of --OR2, C(O)N(R2).sub.2, S(O).sub.nN(R2).sub.2, CN,
SR2, SO.sub.nR2, COR2, CO.sub.2R2 or NR2C(O)R2, R5, and R7;
[0121] R4 is N(R8).sub.2, NHOH, N(R8)COR8, NR8S(O).sub.nR8,
NR8C[.dbd.N(R8)]N(R8).sub.2, N(R8)N(R8)C(O)R8,
NR8PO.sub.nN(R8).sub.2, NR8PO.sub.nOR8, OH, OR8, OC(O)R8, OC(S)R8,
OC(O)N(R8).sub.2, OC(S)N(R8).sub.2, OPO.sub.n(R8).sub.2, R2OH,
R2-halo, CN, COR8, CO.sub.2R8, CON(R8).sub.2, C(O)N(R8)N(R8).sub.2,
S(O).sub.nR8, SO.sub.2N(R8).sub.2, halo, NO.sub.2, or SR8;
[0122] R5 is OH, OR8, N(R8).sub.2, NHOH, N(R8)COR8, NR8S(O)nR8,
NR8C[.dbd.N(R8)]N(R8).sub.2, N(R8)N(R8)C(O)R8, NR8POnNR8R8,
NR8POnOR8, R2OH, R2-halo, CN, COR8, CO.sub.2R8, CON(R8).sub.2,
C(O)N(R8)N(R8).sub.2, S(O)nR8, SO.sub.2N(R8).sub.2, halo, NO.sub.2,
SR8, oxo, .dbd.N--OH, .dbd.N--OR8, .dbd.N--N(R8).sub.2, .dbd.NR8,
.dbd.NNR8C(O)N(R8).sub.2, .dbd.NNR8C(O)OR8,
.dbd.NNR8S(O)nN(R8).sub.2, .dbd.NNR8S (O).sub.n(8), or
.dbd.NNR8S(O)n(R8),
[0123] or R5 is C2-C6 alkenyl, C2-C6 alkynyl, C3-C8 cycloalkyl,
C5-C8 cycloalkenyl, or heterocyclo, which groups may be optionally
substituted with one or more substituents selected from the group
consisting of --OR2, C(O)NR2, S(O).sub.nN(R2).sub.2, CN, SR2,
SO.sub.nR2, COR2, CO.sub.2R2 or NR2C(O)R2, R5, and R7,
[0124] or R5 is C(O)R2, C(O)R3, C(O)R6, C(S)R2, C(S)R3, C(S)R6,
C(Z)N(R2).sub.2, C(Z)N(R3).sub.2, C(Z)N(R6).sub.2, C(Z)NR2R3,
C(Z)NR2R6, C(Z)NR3R6, CO.sub.2R2; provided R2 is not H; CO.sub.2R3,
or CO.sub.2R6;
[0125] R6 is aryl or heteroaryl, wherein said aryl or heteroaryl
may be optionally substituted with one or more groups selected from
the group consisting of aryl, heteroaryl, R2, R3, and R4;
[0126] R7 is C(O)R2, C(O)R3, C(O)R6, C(S)R2, C(S)R3, C(S)R6,
C(Z)N(R2).sub.2, C(Z)N(R3).sub.2, C(Z)N(R6).sub.2, C(Z)NR2R3,
C(Z)NR2R6, C(Z)NR3R6, CO.sub.2R2; provided R2 is not H; CO.sub.2R3,
or CO.sub.2R6
[0127] R8 is H and C1-C6 alkyl optionally substituted by R3, R5, or
R6,
[0128] or R8 is C2-C6 alkenyl, C2-C6 alkynyl, C3-C8 cycloalkyl,
C5-C8 cycloalkenyl, and heterocyclo, which groups may be optionally
substituted with one or more substituents selected from the group
consisting of --OR2, C(O)NHR2, S(O)nN(R2)(R2), CN, SR2, SOnR2,
COR2, CO2R2 or NR2C(O)R2, R5, and R7;
[0129] or R8 is aryl or heteroaryl, wherein said aryl or heteroaryl
may be optionally substituted with one or more groups selected from
the group consisting of aryl, heteroaryl, R2, R3, R4, and R6;
[0130] Z is O, S;
[0131] each n is independently an integer between 1-2;
[0132] its stereoisomeric forms; and its pharmacologically
acceptable salts.
[0133] In another preferred embodiment, the invention also provides
an HIV protease inhibitor represented by a formula: X-A-B-A'-X'
[0134] wherein:
[0135] X is tetrahydrofurodihydrofuranyl,
tetrahydrofurotetrahydrofuranyl, tetrahydropyranotetrahydrofuranyl
or tetrahydropyranodihydrofuranyl;
[0136] A is OCONH;
[0137] B is ##STR8## wherein D is alkyl, alkenyl, alkynyl, aryl,
cycloalkyl, or aralkyl optionally substituted by alkyl, halo,
nitro, cyano, CF.sub.3, O-alkyl or S-alkyl;
[0138] A' is N(D')E', wherein D' is alkyl, alkenyl, alkynyl aryl,
cycloalkyl, or aralkyl optionally substituted by alkyl, halo, or
CF3, and E' is --SO.sub.2--;
[0139] X' is selected from the group consisting of aryl and
heteroaryl, which are substituted with one or more groups selected
from the group consisting of:
[0140] OR3, OR6, OR7, or OR2 provided R2 is not H or unsubstituted
alkyl;
[0141] alkyl substituted by R3, R5, or R6 provided R5 is not
halo;
[0142] C2-C6 alkenyl, C2-C6 alkynyl, C3-C8 cycloalkyl, C5-C8
cycloalkenyl, and heterocyclo, which groups may be optionally
substituted with one or more substituents selected from the group
consisting of --OR2, C(O)NHR2, S(O)nN(R2)(R2), CN, SR2, SOnR2,
COR2, CO.sub.2R2 or NR2C(O)R2, R5, and R7;
[0143] aryl or heteroaryl, wherein said aryl or heteroaryl may be
optionally substituted with one or more groups selected from the
group consisting of aryl, heteroaryl, R2, R3, R4, and R6;
[0144] C3-C7 cycloalkyl substituted by R2, R3, R5, or R6; provided
R2 is not H;
[0145] CO.sub.2H, or R7 where Z=N, O, S and provided R2 is not H or
unsubstituted alkyl
[0146] NR3R3, NR6R6, NR7R7, NR3R6, NR6R7, NR3R7, NR2R3, NR2R6,
[0147] NR2R7, NR2R2 provided R2 is not H or unsubstituted
alkyl;
[0148] SOnN(R2).sub.2, SOnN(R3).sub.2, SOnN(R6).sub.2,
SOnN(R7).sub.2, SOnNR2R3, SOnNR2R6, SOnNR2R7, SOnNR3R6, SOnNR3R7,
SOnNR6R7, n=1 or 2;
[0149] S(O)nR2, S(O)nR3, S(O)nR6, provided R2 is not H or methyl; n
is 0, 1 or 2;
[0150] R2 is H or C1-C6 alkyl optionally substituted by R3, R5, or
R6,
[0151] R3 is C2-C6 alkenyl, C2-C6 alkynyl, C3-C8 cycloalkyl, C5-C8
cycloalkenyl, and heterocyclo, which groups may be optionally
substituted with one or more substituents selected from the group
consisting of --OR2, C(O)N(R2).sub.2, S(O)nN(R2)(R2), CN, SR2,
SOnR2, COR2, CO.sub.2R2 or NR2C(O)R2, R5, and R7;
[0152] R4 is N(R8).sub.2, NHOH, N(R8)COR8, NR8S(O)nR8,
NR8C[.dbd.N(R8)]N(R8).sub.2, N(R8)N(R8)C(O)R8, NR8POnNR8R8,
NR8POnOR8, OH, OR8, OC(O)R8, OC(S)R8, OC(O)N(R8).sub.2,
OC(S)N(R8).sub.2, OPOn(R8).sub.2R2OH, R2-halo, CN, COR8,
CO.sub.2R8, CON(R8).sub.2, C(O)N(R8)N(R8).sub.2, S(O)nR8,
SO.sub.2N(R8).sub.2, halo, NO.sub.2, or SR8;
[0153] R5 is OH, OR8, N(R8).sub.2, NHOH, N(R8)COR8,
NR8S(O).sub.nR8, NR8C[.dbd.N(R8)]N(R8).sub.2, N(R8)N(R8)C(O)R8,
NR8PO.sub.nN(R8).sub.2, NR8PO.sub.nOR8, R2OH, R2-halo, CN, COR8,
CO.sub.2R8, CON(R8).sub.2, C(O)N(R8)N(R8).sub.2, S(O).sub.nR8,
SO.sub.2N(R8).sub.2, halo, NO.sub.2, SR8, oxo, .dbd.N--OH,
.dbd.N--OR8, .dbd.N--N(R8).sub.2, .dbd.NR8,
.dbd.NNR8C(O)N(R8).sub.2, .dbd.NNR8C(O)OR8,
.dbd.NNR8S(O).sub.nN(R8).sub.2, or .dbd.NNR8S(O).sub.n(R8),
.dbd.NNR8C(O)R8,
[0154] or R5 is C2-C6 alkenyl, C2-C6 alkynyl, C3-C8 cycloalkyl,
C5-C8 cycloalkenyl, or heterocyclo, which groups may be optionally
substituted with one or more substituents selected from the group
consisting of --OR2, C(O)NR2, S(O).sub.nN(R2).sub.2, CN, SR2,
SO.sub.nR2, COR2, CO.sub.2R2 or NR2C(O)R2, R5, and R7,
[0155] or R5 is C(O)R2, C(O)R3, C(O)R6, C(S)R2, C(S)R3, C(S)R6,
C(Z)N(R2).sub.2, C(Z)N(R3).sub.2, C(Z)N(R6).sub.2, C(Z)NR2R3,
C(Z)NR2R6, C(Z)NR3R6, CO.sub.2R2; provided R2 is not H; CO.sub.2R3,
or CO.sub.2R6;
[0156] R6 is aryl or heteroaryl, wherein said aryl or heteroaryl
may be optionally substituted with one or more groups selected from
the group consisting of aryl, heteroaryl, R2, R3, and R4;
[0157] R7 is C(O)R2, C(O)R3, C(O)R6, C(S)R2, C(S)R3, C(S)R6,
C(Z)N(R2).sub.2, C(Z)N(R3).sub.2, C(Z)N(R6).sub.2, C(Z)NR2R3,
C(Z)NR2R6, C(Z)NR3R6, CO.sub.2R2; provided R2 is not H; CO.sub.2R3,
or CO.sub.2R6
[0158] R8 is H or C1-C6 alkyl optionally substituted by R3, R5, or
R6,
[0159] or R8 is C2-C6 alkenyl, C2-C6 alkynyl, C3-C8 cycloalkyl,
C5-C8 cycloalkenyl, or heterocyclo, which groups may be optionally
substituted with one or more substituents selected from the group
consisting of --OR2, C(O)NR2, S(O).sub.nN(R2).sub.2, CN, SR2,
SO.sub.nR2, COR2, CO.sub.2R2 or NR2C(O)R2, R5, and R7,
[0160] or R8 is aryl or heteroaryl, wherein said aryl or heteroaryl
may be optionally substituted with one or more groups selected from
the group consisting of aryl, heteroaryl, R2, R3, R4, and R6;
[0161] Z is O, S;
[0162] each n is independently an integer between 1-2; its
stereoisomeric forms;
[0163] and its pharmacologically acceptable salts.
[0164] In another preferred embodiment, the invention also provides
an HIV protease inhibitor represented by a formula: X-A-B-A'-X'
[0165] wherein:
[0166] X is tetrahydrofurotetrahydrofuranyl;
[0167] A is OCONH;
[0168] B is ##STR9## wherein D is benzyl
[0169] A' is N(D')E', wherein D' is isobutyl and E' is
--SO.sub.2--;
[0170] X' is selected from the group consisting of aryl and
heteroaryl, which are substituted with one or more groups selected
from the group consisting of:
[0171] OR3, OR6, OR7, OR2 provided R2 is not H or unsubstituted
alkyl;
[0172] alkyl substituted by R3, R5, R6 provided R5 is not halo;
[0173] C2-C6 alkenyl, C2-C6 alkynyl, C3-C8 cycloalkyl, C5-C8
cycloalkenyl, and heterocyclo, which groups may be optionally
substituted with one or more substituents selected from the group
consisting of --OR2, C(O)NHR2, S(O)nN(R2)(R2), CN, SR2, SOnR2,
COR2, CO.sub.2R2 NR2C(O)R2, R5, and R7;
[0174] aryl or heteroaryl, wherein said aryl or heteroaryl may be
optionally substituted with one or more groups selected from the
group consisting of aryl, heteroaryl, R2, R3, R4, and R6;
[0175] C3-C7 cycloalkyl substituted by R2, R3, R5, R6; provided R2
is not H;
[0176] CO.sub.2H, R7 where Z=N, O, or S provided R2 is not H or
unsubstituted alkyl
[0177] NR3R3, NR6R6, NR7R7, NR3R6, NR6R7, NR3R7, NR2R3, NR2R6,
[0178] NR2R7, or NR2R2 provided R2 is not H or unsubstituted
alkyl;
[0179] SOnN(R2).sub.2, SOnN(R3).sub.2, SOnN(R6).sub.2
SOnN(R7).sub.2, SOnNR2R3, SOnNR2R6, SOnNR2R7, SOnNR3R6, SOnNR3R7,
or SOnNR6R7, wherein n=1 or 2;
[0180] S(O)nR2, S(O)nR3, S(O)nR6, provided R2 is not H or methyl;
wherein n is 0, 1 or 2;
[0181] R2 is H and C1-C6 alkyl optionally substituted by R3, R5, or
R6,
[0182] R3 is C2-C6 alkenyl, C2-C6 alkynyl, C3-C8 cycloalkyl, C5-C8
cycloalkenyl, or heterocyclo, which groups may be optionally
substituted with one or more substituents selected from the group
consisting of --OR2, C(O)N(R2).sub.2, S(O).sub.nN(R2).sub.2, CN,
SR2, SO.sub.nR2, COR2, CO.sub.2R2 or NR2C(O)R2, R5, and R7;
[0183] R4 is N(R8).sub.2, NHOH, N(R8)COR8, NR8S(O).sub.nR8,
NR8C[.dbd.N(R8)]N(R8).sub.2, N(R8)N(R8)C(O)R8,
NR8PO.sub.nN(R8).sub.2, NR8PO.sub.nOR8, OH, OR8, OC(O)R8, OC(S)R8,
OC(O)N(R8).sub.2, OC(S)N(R8).sub.2, OPO.sub.n(R8).sub.2, R2OH,
R2-halo, CN, COR8, CO.sub.2R8, CON(R8).sub.2, C(O)N(R8)N(R8).sub.2,
S(O).sub.nR8, SO.sub.2N(R8).sub.2, halo, NO.sub.2, or SR8;
[0184] R5 is OH, OR8, N(R8).sub.2, NHOH, N(R8)COR8,
NR8S(O).sub.nR8, NR8C[.dbd.N(R8)]N(R8).sub.2, N(R8)N(R8)C(O)R8,
NR8PO.sub.nN(R8).sub.2 NR8PO.sub.nOR8, R2OH, R2-halo, CN, COR8,
CO.sub.2R8, CON(R8).sub.2, C(O)N(R8)N(R8).sub.2, S(O).sub.nR8,
SO.sub.2N(R8).sub.2, halo, NO.sub.2, SR8, oxo, .dbd.N--OH,
.dbd.N--OR8, .dbd.N--N(R8).sub.2, .dbd.NR8,
.dbd.NNR8C(O)N(R8).sub.2, .dbd.NNR8C(O)OR8,
.dbd.NNR8S(O).sub.nN(R8).sub.2, or .dbd.NNR8S(O).sub.n(R8),
.dbd.NNR8C(O)R8,
[0185] or R5 is C2-C6 alkenyl, C2-C6 alkynyl, C3-C8 cycloalkyl,
C5-C8 cycloalkenyl, or heterocyclo, which groups may be optionally
substituted with one or more substituents selected from the group
consisting of --OR2, C(O)NR2, S(O).sub.nN(R2).sub.2, CN, SR2,
SO.sub.nR2, COR2, CO.sub.2R2 or NR2C(O)R2, R5, and R7,
[0186] or R5 is C(O)R2, C(O)R3, C(O)R6, C(S)R2, C(S)R3, C(S)R6,
C(Z)N(R2).sub.2, C(Z)N(R3).sub.2, C(Z)N(R6).sub.2, C(Z)NR2R3,
C(Z)NR2R6, C(Z)NR3R6, CO.sub.2R2; provided R2 is not H; CO.sub.2R3,
or CO.sub.2R6;
[0187] R6 is aryl or heteroaryl, wherein said aryl or heteroaryl
may be optionally substituted with one or more groups selected from
the group consisting of aryl, heteroaryl, R2, R3, and R4;
[0188] R7 is C(O)R2, C(O)R3, C(O)R6, C(S)R2, C(S)R3, C(S)R6,
C(Z)N(R2).sub.2, C(Z)N(R3).sub.2, C(Z)N(R6).sub.2, C(Z)NR2R3,
C(Z)NR2R6, C(Z)NR3R6, CO.sub.2R2; provided R2 is not H; CO.sub.2R3,
or CO.sub.2R6
[0189] R8 is H or C1-C6 alkyl optionally substituted by R3, R5, or
R6,
[0190] or R8 is C2-C6 alkenyl, C2-C6 alkynyl, C3-C8 cycloalkyl,
C5-C8 cycloalkenyl, or heterocyclo, which groups may be optionally
substituted with one or more substituents selected from the group
consisting of --OR2, C(O)NR2, S(O).sub.nN(R2).sub.2, CN, SR2,
SO.sub.nR2, COR2, CO.sub.2R2 or NR2C(O)R2, R5, and R7,
[0191] or R8 is aryl or heteroaryl, wherein said aryl or heteroaryl
may be optionally substituted with one or more groups selected from
the group consisting of aryl, heteroaryl, R2, R3, R4, and R6;
[0192] Z is O, S;
[0193] each n is independently an integer between 1-2; its
stereoisomeric forms; and its pharmacologically acceptable
salts.
[0194] Preferably, X is ##STR10##
[0195] wherein A2, B2, and C are each independently O, NR2, or
S;
[0196] D2 is CH or N; and
[0197] wherein any ring carbon is optionally substituted by R2, R3,
R5, or R6.
[0198] Preferably, X is ##STR11##
[0199] wherein
[0200] A3 is H, F or alkoxy;
[0201] B3 is F, alkoxy, lower alkyl, or A and B can form a 3-7
membered heterocyclic ring;
[0202] Z is O, NR2, or S;
[0203] n is an integer between 1-3; and
[0204] wherein any ring carbon is optionally substituted by R2, R3,
R5, R6.
[0205] With regard to X, X may also be a 5-7 membered non-aromatic
monocyclic heterocycle, wherein said heterocycle is optionally
fused or bridged with one or more 3-7 membered non-aromatic
monocyclic heterocycle to form a polycyclic system, wherein any of
said heterocyclic ring systems contains one or more heteroatoms
selected from O, N, S, or P; wherein any nitrogen forming part of
the heterocycles may optionally be substituted by R2, R3, R6, R7 or
O; wherein any sulfur may be optionally be substituted by one or
two oxygen atoms; wherein any P may be optionally be substituted by
one or more of O NR2, or S, and any of said ring systems optionally
contains 1 to 6 substituents selected from the group consisting of
R2, R3, R5, and R6.
[0206] X may also be ##STR12##
[0207] wherein, Y is O, NH, or S; Z is O, NH, or S; and wherein any
ring carbon is optionally substituted by R2, R3, R5, or R6.
[0208] X may also be ##STR13##
[0209] wherein G is C, O, NR2, or S; n is an integer between 1-2;
and wherein any ring carbon is optionally substituted by R2, R3,
R5, or R6.
[0210] X may also be ##STR14##
[0211] wherein J is independently CH.sub.2, or O, and wherein any
ring carbon is optionally substituted by R2, R3, R5, or R6.
[0212] X may also be ##STR15##
[0213] wherein any ring carbon is optionally substituted by R2, R3,
R5, or R6.
[0214] X may also be ##STR16##
[0215] wherein each L is independently H, lower alkyl, oxo, or L
forms a carbocyclic or heterocyclic ring with M; each M is
independently H, OH, chloro, fluoro, or M forms a carbocyclic or
heterocyclic ring with Q, provided that if one M is OH, the other M
is not OH; Q is H, OH, amino, lower alkyl, alkylamino, alkoxy,
halo, or forms a 3-7-membered carbocyclic or heterocyclic ring
together with T; each F is independently H, OH, lower alkyl, halo,
or spirocylopropyl, provided that if one R is OH, the other R is
not OH; T is H or F, or T forms a carbocyclic or heterocyclic ring
together with F.
[0216] X may also be ##STR17##
[0217] wherein A2, B2, and C' are each independently O, NR2, or S;
D2 is CH or N; and n is an integer between 1 and 2.
[0218] X may also be ##STR18##
[0219] wherein A3 is H, F or alkoxy; B3 is F, alkoxy, lower alkyl,
or A3 and B3 can form a 3-7 membered heterocyclic ring; Z' is O,
NR2, or S; and n is an integer between 1-3.
[0220] X is preferably tetrahydrofurodihydrofuranyl,
tetrahydrofuro-tetrahydrofuranyl,
tetrahydropyrano-tetrahydrofuranyl or
tetrahydropyranodihydrofuranyl. More preferably, X is
tetrahydrofurotetrahydro-furanyl.
[0221] With regard to A, A may be ZCZNH, ZCOCONH, ZS(O).sub.2NH,
ZP(O)(V)NH, CONH, COCONH, S(O).sub.2NH, P(O)(V)NH, wherein Z is
NR2, O, S, or C(R2).sub.2, and V is OR2 or NR2. A is preferably
OCONH.
[0222] With regard to B, B may be ##STR19## wherein D is selected
from alkyl, alkenyl, alkynyl, aryl, cycloalkyl, or aralkyl
optionally substituted with one or more groups selected from alkyl,
halo, nitro, cyano, CF.sub.3, C3-C7 cycloalkyl, C5-C7 cycloalkenyl,
R6, OR2, SR2, NHR2, OR3, SR3, NHR3, OR6, SR6, or NHR6.
[0223] With regard to A', A' may be N(D')E', wherein D' is selected
from alkyl, alkenyl, alkynyl, aryl, cycloalkyl, or aralkyl
optionally substituted by alkyl, halo, nitro, cyano, CF.sub.3,
O-alkyl, or S-alkyl, and E' is --CO-- or --SO.sub.2--. Preferably,
D' is alkyl, alkenyl, alkynyl aryl, cycloalkyl, or aralkyl
optionally substituted by alkyl, halo, or CF.sub.3, and E' is
--SO.sub.2--. More preferably, D' is isobutyl and E' is
--SO.sub.2--.
[0224] With regard to X', X'is selected from the group consisting
of aryl and heteroaryl, which are substituted with one or more of
the following groups: OR3, OR6, OR7, OR2 provided R2 is not H or
unsubstituted alkyl; alkyl substituted by R3, R5, R6 provided R5 is
not halo; C2-C6 alkenyl, C2-C6 alkynyl, C3-C8 cycloalkyl, C5-C8
cycloalkenyl, and heterocyclo, which groups may be optionally
substituted with one or more substituents selected from R5; aryl or
heteroaryl, wherein said aryl or heteroaryl may be optionally
substituted with one or more groups selected from the group
consisting of aryl, heteroaryl, R2, R3, R4, and R6; C3-C7
cycloalkyl substituted by R2, R3, R5, R6; provided R2 is not H;
CO.sub.2H or R7; provided R8 is not H or unsubstituted alkyl;
NR8R8, NR7R8, NR7R7; provided R8 is not H or unsubstituted alkyl;
SO.sub.nN(R8).sub.2, SO.sub.nNR7R8, SR8, S(O).sub.nR8, provided R8
is not H or methyl; and n is 1 or 2.
[0225] X' may also be ##STR20##
[0226] wherein said groups are substituted with one or more of the
following groups: OR3, OR6, OR7, OR2 provided R2 is not H or
unsubstituted alkyl; alkyl substituted by R3, R5, R6 provided R5 is
not halo; C2-C6 alkenyl, C2-C6 alkynyl, C3-C8 cycloalkyl, C5-C8
cycloalkenyl, and heterocyclo, which groups may be optionally
substituted with one or more substituents selected from R5; aryl or
heteroaryl, wherein said aryl or heteroaryl may be optionally
substituted with one or more groups selected from the group
consisting of aryl, heteroaryl, R2, R3, R4, and R6; C3-C7
cycloalkyl substituted by R2, R3, R5, R6; provided R2 is not H;
CO.sub.2H or R7; provided R8 is not H or unsubstituted alkyl;
NR8R8, NR7R8, NR7R7; provided R8 is not H or unsubstituted alkyl;
SO.sub.nN(R8).sub.2, SO.sub.nNR7R8, SR8, S(O).sub.nR8, provided R8
is not H or methyl; and n is 1 or 2.
[0227] X' may also be ##STR21## wherein G' and R' cannot both be H;
G' and R' are each independently: H or alkyl substituted by R3, R5,
R6 provided R5 is not halo; C2-C6 alkenyl, C2-C6 alkynyl, C3-C8
cycloalkyl, C5-C8 cycloalkenyl, and heterocyclo, which groups may
be optionally substituted with one or more substituents selected
from the group consisting of --OR2, C(O)N(R2).sub.2,
S(O).sub.nN(R2).sub.2, CN, SR2, SO.sub.nR2, COR2, CO.sub.2R2 or
NR2C(O)R2, R5, and R7; aryl or heteroaryl, wherein said aryl or
heteroaryl may be optionally substituted with one or more groups
selected from the group consisting of aryl, heteroaryl, R2, R3, R4,
and R6; C3-C7 cycloalkyl substituted by R2, R3, R5, R6; provided R2
is not H; CO.sub.2H or R7 provided R2 is not H or unsubstituted
alkyl; SO.sub.nN(R8).sub.2, SO.sub.nNR7R8, SR8, S(O).sub.nR8,
provided R8 is not H or methyl; and n is 1 or 2; and X'' is
selected from O or NR''; wherein R'' is H or alkyl optionally
substituted by R3, R5, R6; C2-C6 alkenyl, C2-C6 alkynyl, C3-C8
cycloalkyl, C5-C8 cycloalkenyl, and heterocyclo, which groups may
be optionally substituted with one or more substituents selected
from the group consisting of --OR2, C(O)N(R2).sub.2,
S(O).sub.nN(R2).sub.2, CN, SR2, SO.sub.nR2, COR2, CO.sub.2R2 or
NR2C(O)R2, R5, and R7; aryl or heteroaryl, wherein said aryl or
heteroaryl may be optionally substituted with one or more groups
selected from the group consisting of aryl, heteroaryl, R2, R3, R4,
and R6; C3-C7 cycloalkyl optionally substituted by R2, R3, R5, R6;
R7; NR3R3, NR6R6, NR7R7, NR3R6, NR6R7, NR3R7, NR2R3, NR2R6, NR2R7,
NR2R2; SO.sub.nN(R2).sub.2, SO.sub.nN(R3).sub.2,
SO.sub.nN(R6).sub.2, SO.sub.nN(R7).sub.2, SO.sub.nNR2R3,
SO.sub.nNR2R6, SO.sub.nNR2R7, SO.sub.nNR3R6, SO.sub.nNR3R7,
SO.sub.nNR6R7; S(O).sub.mR2, S(O).sub.mR3, S(O).sub.mR6, provided
R2 is not H; and m is 0, 1 or 2.
[0228] X' may also be ##STR22##
[0229] wherein B' and B'' cannot both be H or methyl; B' and B''
are independently: H or alkyl optionally substituted by R3, R5, R6;
C2-C6 alkenyl, C2-C6 alkynyl, C3-C8 cycloalkyl, C5-C8 cycloalkenyl,
and heterocyclo, which groups may be optionally substituted with
one or more substituents selected from the group consisting of
--OR2, C(O)N(R2).sub.2, S(O).sub.nN(R2).sub.2, CN, SR2, SO.sub.nR2,
COR2, CO.sub.2R2 or NR2C(O)R2, R5, and R7; aryl or heteroaryl,
wherein said aryl or heteroaryl may be optionally substituted with
one or more groups selected from the group consisting of aryl,
heteroaryl, R2, R3, R4, and R6; C3-C7 cycloalkyl optionally
substituted by R2, R3, R5, R6; CO.sub.2H or R7;
SO.sub.nN(R2).sub.2, SO.sub.nN(R3).sub.2, SO.sub.nN(R6).sub.2,
SO.sub.nN(R7).sub.2, SO.sub.nNR2R3, SO.sub.nNR2R6, SO.sub.nNR2R7,
SO.sub.nNR3R6, SO.sub.nNR3R7, SO.sub.nNR6R7; S(O).sub.mR2,
S(O).sub.mR3, S(O).sub.mR6; SO.sub.nN(R8).sub.2, SO.sub.nNR7R8,
SR8, S(O).sub.nR8, provided R8 is not H or methyl; and n is 1 or 2;
and m is 0, 1 or 2; Z'' is O, NR9; R9 is alkyl optionally
substituted by R3, R5, R6; C2-C6 alkenyl, C2-C6 alkynyl, C3-C8
cycloalkyl, C5-C8 cycloalkenyl, and heterocyclo, which groups may
be optionally substituted with one or more substituents selected
from the group consisting of --OR2, C(O)N(R2).sub.2,
S(O).sub.nN(R2).sub.2, CN, SR2, SO.sub.nR2, COR2, CO.sub.2R2 or
NR2C(O)R2, R5, and R7; aryl or heteroaryl, wherein said aryl or
heteroaryl may be optionally substituted with one or more groups
selected from the group consisting of aryl, heteroaryl, R2, R3, R4,
and R6; C3-C7 cycloalkyl optionally substituted by R2, R3, R5, R6;
CO.sub.2H or R7; NR3R3, NR6R6, NR7R7, NR3R6, NR6R7, NR3R7, NR2R3,
NR2R6, NR2R7, NR2R2; SO.sub.nN(R2).sub.2, SO.sub.nN(R3).sub.2,
SO.sub.nN(R6).sub.2, SO.sub.nN(R7).sub.2, SO.sub.nNR2R3,
SO.sub.nNR2R6, SO.sub.nNR2R7, SO.sub.nNR3R6, SO.sub.nNR3R7,
SO.sub.nNR6R7; S(O).sub.mR2, S(O).sub.mR3, S(O).sub.mR6, provided
R2 is not H; and m is 0, 1 or 2.
[0230] X' may also be ##STR23##
[0231] wherein R10 is alkyl substituted by R3, R5, R6 provided R5
is not halo; C2-C6 alkenyl, C2-C6 alkynyl, C3-C8 cycloalkyl, C5-C8
cycloalkenyl, and heterocyclo, which groups may be optionally
substituted with one or more substituents selected from the group
consisting of --OR2, C(O)N(R2).sub.2, S(O).sub.nN(R2).sub.2, CN,
SR2, SO.sub.nR2, COR2, CO.sub.2R2 or NR2C(O)R2, R5, and R7; aryl or
heteroaryl, wherein said aryl or heteroaryl may be optionally
substituted with one or more groups selected from the group
consisting of aryl, heteroaryl, R2, R3, R4, and R6; C3-C7
cycloalkyl substituted by R2, R3, R5, R6; provided R2 is not H; R7
provided Z is N, O, S and provided R2 is not H or unsubstituted
alkyl; and F' is O or S.
[0232] X' may also be ##STR24##
[0233] Wherein U and U' are each independently H or alkyl
substituted by R3, R5, R6; C2-C6 alkenyl, C2-C6 alkynyl, C3-C8
cycloalkyl, C5-C8 cycloalkenyl, and heterocyclo, which groups may
be optionally substituted with one or more substituents selected
from the group consisting of --OR2, C(O)N(R2).sub.2,
S(O).sub.nN(R2).sub.2, CN, SR2, SO.sub.nR2, COR2, CO.sub.2R2 or
NR2C(O)R2, R5, and R7; aryl or heteroaryl, wherein said aryl or
heteroaryl may be optionally substituted with one or more groups
selected from the group consisting of aryl, heteroaryl, R2, R3, R4,
and R6; C3-C7 cycloalkyl substituted by R2, R3, R5, R6; CO.sub.2H,
R7; SO.sub.nN(R8).sub.2, SO.sub.nNR7R8, SR8, S(O).sub.nR8, provided
R8 is not H or methyl; and n is 1 or 2; SO.sub.nN(R2).sub.2,
SOnN(R3).sub.2, SO.sub.nN(R6).sub.2, SO.sub.nN(R7).sub.2,
SO.sub.nNR2R3, SO.sub.nNR2R6, SO.sub.nNR2R7, SO.sub.nNR3R6,
SO.sub.nNR3R7, SO.sub.nNR6R7, wherein n=1 or 2; S(O).sub.mR2,
S(O).sub.mR3, S(O).sub.mR6, provided R2 is not H; and n is 0, 1 or
2.
[0234] U'' and U''' are each independently H, OR3, OR6, OR7, OR2;
alkyl substituted by R3, R5, R6; C2-C6 alkenyl, C2-C6 alkynyl,
C3-C8 cycloalkyl, C5-C8 cycloalkenyl, and heterocyclo, which groups
may be optionally substituted with one or more substituents
selected from the group consisting of --OR2, C(O)N(R2).sub.2,
S(O).sub.nN(R2).sub.2, CN, SR2, SO.sub.nR2, COR2, CO.sub.2R2 or
NR2C(O)R2, R5, and R7; aryl or heteroaryl, wherein said aryl or
heteroaryl may be optionally substituted with one or more groups
selected from the group consisting of aryl, heteroaryl, R2, R3, R4,
and R6; C3-C7 cycloalkyl substituted by R2, R3, R5, R6; CO.sub.2H
or R7; NR3R3, NR6R6, NR7R7, NR3R6, NR6R7, NR3R7, NR2R3, NR2R6,
NR2R7, NR2R2; SO.sub.nN(R8).sub.2, SO.sub.nNR7R8, SR8,
S(O).sub.nR8, provided R8 is not H or methyl; and n is 1 or 2;
SO.sub.nN(R2).sub.2, SO.sub.nN(R3).sub.2, SO.sub.nN(R6).sub.2,
SO.sub.nN(R7).sub.2, SO.sub.nNR2R3, SO.sub.nNR2R6, SO.sub.nNR2R7,
SO.sub.nNR3R6, SO.sub.nNR3R7, SO.sub.nNR6R7; S(O).sub.mR2,
S(O).sub.mR3, S(O).sub.mR6, provided R2 is not H; and m is 0, 1 or
2; U and U' cannot both be H unless one of U'' and U''' is not H;
U'' and U''' cannot both be H unless one of U and U' is not H; M'
is O, NR9, or NH, except where R9 is CO.sub.2H; Z''' is O or NR9;
Q' is O, NR9, or CU''U'''.
[0235] R9 is alkyl optionally substituted by R3, R5, R6; C2-C6
alkenyl, C2-C6 alkynyl, C3-C8 cycloalkyl, C5-C8 cycloalkenyl, and
heterocyclo, which groups may be optionally substituted with one or
more substituents selected from the group consisting of --OR2,
C(O)N(R2).sub.2, S(O).sub.nN(R2).sub.2, CN, SR2, SO.sub.nR2, COR2,
CO.sub.2R2 or NR2C(O)R2, R5, and R7; aryl or heteroaryl, wherein
said aryl or heteroaryl may be optionally substituted with one or
more groups selected from the group consisting of aryl, heteroaryl,
R2, R3, R4, and R6; C3-C7 cycloalkyl optionally substituted by R2,
R3, R5, R6; CO.sub.2H or R7; NR3R3, NR6R6, NR7R7, NR3R6, NR6R7,
NR3R7, NR2R3, NR2R6, NR2R7, NR2R2; SO.sub.nN(R8).sub.2,
SO.sub.nNR7R8, SR8, S(O).sub.nR8, provided R8 is not H or methyl;
and n is 1 or 2; SO.sub.nN(R2).sub.2, SO.sub.nN(R3).sub.2,
SO.sub.nN(R6).sub.2, SO.sub.nN(R7).sub.2, SO.sub.nNR2R3,
SO.sub.nNR2R6, SO.sub.nNR2R7, SO.sub.nNR3R6, SO.sub.nNR3R7,
SO.sub.nNR6R7; S(O).sub.mR2, S(O).sub.mR3, S(O).sub.mR6, provided
R2 is not H; and m is 0, 1 or 2.
[0236] Preferably, R is H or alkyl, aryl, alkenyl, alkynyl,
cycloalkyl, cycloalkenyl, heterocyclo, heteroaryl; optionally
substituted by halo, hydroxy, alkoxy, aryloxy, cycloalkoxy,
heteroaryloxy, cyano, nitro, alkylthio, arylthio, cycloalkylthio,
amino, or mono- or dialkylamino, mono- or diarylamino, mono- or
di-cycloalkylamino, mono- or di-heteroarylamino, alkanoyl,
cycloalkanoyl, aroyl, heteroaroyl, carboxamido, mono- or
dialkylcarboxamido, mono- or diarylcarboxamido, sulfonamido, mono-
or dialkylsulfonamido, mono- or diarylsulfonamido, alkylsulfinyl,
alkylsulfonyl, arylsulfinyl, arylsulfonyl, cycloalkylsulfinyl,
cycloalkylsulfonyl, heteroarylsulfinyl, heteroarylsulfonyl.
[0237] Prererably, R2 is H or C1-C6 alkyl; optionally substituted
by C2-C6 alkenyl, C2-C6 alkynyl, C3-C8 cycloalkyl, C5-C8
cycloalkenyl, heterocyclo; which groups may be optionally
substituted with one or more substituents selected from the group
consisting of halo, OR, ROH, R-halo, NO.sub.2, CN, CO.sub.nR,
CON(R).sub.2, C(S)R, C(S)N(R).sub.2, SO.sub.nN(R).sub.2, SR,
SO.sub.nR, N(R).sub.2, N(R)CO.sub.nR, NRS(O).sub.nR,
NRC[.dbd.N(R)]N(R).sub.2, N(R)N(R)CO.sub.nR, NRPO.sub.nN(R).sub.2,
NRPO.sub.nOR, oxo, .dbd.N--OR, .dbd.N--N(R).sub.2, .dbd.NR,
.dbd.NNRC(O)N(R).sub.2, .dbd.NNRCO.sub.nR,
.dbd.NNRS(O).sub.nN(R).sub.2, or .dbd.NNRS(O).sub.n(R); or R2 is
C1-C6 alkyl; substituted by aryl or heteroaryl; which groups may be
optionally substituted with one or more substituents selected from
the group consisting of halo, OR, ROH, R-halo, NO.sub.2, CN,
CO.sub.nR, CON(R).sub.2, C(S)R, C(S)N(R).sub.2, SO.sub.nN(R).sub.2,
SR, SO.sub.nR, N(R).sub.2, N(R)CO.sub.nR, NRS(O).sub.nR,
NRC[.dbd.N(R)]N(R).sub.2, N(R)N(R)CO.sub.nR, NRPO.sub.nN(R).sub.2,
NRPO.sub.nOR; or R2 is C1-C6 alkyl; optionally substituted by halo,
OR, ROH, R-halo, NO.sub.2, CN, CO.sub.nR, CON(R).sub.2, C(S)R,
C(S)N(R).sub.2, SO.sub.nN(R).sub.2, SR, SO.sub.nR, N(R).sub.2,
N(R)CO.sub.nR, NRS(O).sub.nR, NRC[.dbd.N(R)]N(R).sub.2,
N(R)N(R)CO.sub.nR, NRPO.sub.nN(R).sub.2, NRPO.sub.nOR, oxo,
.dbd.N--OR, .dbd.N--N(R).sub.2, .dbd.NR, .dbd.NNRC(O)N(R).sub.2,
.dbd.NNRCOnR, .dbd.NNRS(O)nN(R).sub.2, or .dbd.NNRS(O)n(R).
[0238] Preferably, R3 is C2-C6 alkenyl, C2-C6 alkynyl, C3-C8
cycloalkyl, C5-C8 cycloalkenyl, or heterocyclo; which groups may be
optionally substituted with one or more substituents selected from
the group consisting of halo, OR2, R2--OH, R2-halo, NO.sub.2, CN,
CO.sub.nR2, C(O)N(R2).sub.2, C(O)N(R2)N(R2).sub.2, C(S)R2,
C(S)N(R2).sub.2, S(O)nN(R2).sub.2, SR2, SO.sub.nR2, N(R).sub.2,
N(R2)CO.sub.nR2, NR2S(O).sub.nR2, NR2C[.dbd.N(R2)]N(R2).sub.2,
N(R2)N(R2)CO.sub.nR2, NR2PO.sub.nN(R2).sub.2, NR2PO.sub.nOR2, oxo,
.dbd.N--OR2, .dbd.N--N(R2).sub.2, .dbd.NR2,
.dbd.NNRC(O)N(R2).sub.2, .dbd.NNR2C(O).sub.nR2,
.dbd.NNR2S(O).sub.nN(R2).sub.2, or .dbd.S(O).sub.n(R2).
[0239] Preferably, R4 is halo, OR8, R2--OH, R3-OH, R2-halo,
R3-halo, NO.sub.2, CN, CO.sub.nR8, CO.sub.nR8, CON(R8).sub.2,
C(O)N(R8)N(R8).sub.2, C(S)R8, C(S)N(R8).sub.2, SOnN(R8).sub.2, SR8,
SO.sub.nR8, N(R8).sub.2, N(R8)CO.sub.nR8, NR8S(O).sub.nR8,
NR8C[.dbd.N(R8)]N(R8).sub.2, N(R8)N(R8)CO.sub.nR8,
NR8PO.sub.nN(R8).sub.2, NR8PO.sub.nOR8, OC(O)R2, OC(S)R8,
OC(O)N(R8).sub.2, OC(S)N(R8).sub.2, OPO.sub.n(R8).sub.2.
[0240] Preferably, R5 is OR8, N(R8).sub.2, NHOH, N(R8)COR8,
NR8S(O).sub.nR8, NR8C[.dbd.N(R8)]N(R8).sub.2, N(R8)N(R8)C(O)R8,
NR8PO.sub.nN(R8).sub.2, NR8PO.sub.nOR8, R2OH, R3-OH, R2-halo,
R3-halo, CN, CO.sub.nR8; provided that when n=2, R8 is not H;
CON(R8).sub.2, C(O)N(R8)N(R8).sub.2, C(S).sub.nR8, C(S)N(R8).sub.2,
S(O).sub.nR8, SO.sub.nN(R8).sub.2, halo, NO.sub.2, SR8, oxo,
.dbd.N--OH, .dbd.N--OR8, .dbd.N--N(R8).sub.2, .dbd.NR8,
.dbd.NNR8C(O)N(R8).sub.2, .dbd.NNR8C(O).sub.nR8, .dbd.NNR8
S(O).sub.nN(R8).sub.2, or .dbd.NNR8S(O).sub.n(R8), or R3.
[0241] Preferably, R6 is aryl or heteroaryl, wherein said aryl or
heteroaryl may be optionally substituted with one or more groups
selected from aryl, heteroaryl, R2, R3, halo, OR2, R2OH, R2-halo,
NO.sub.2, CN, CO.sub.nR2, C(O)N(R2).sub.2, C(O)N(R2)N(R2).sub.2,
C(S)R2, C(S)N(R2).sub.2, S(O).sub.nN(R2).sub.2, SR2, SO.sub.nR2,
N(R).sub.2, N(R2)CO.sub.nR, NR2S(O).sub.nR2,
NR2C[.dbd.N(R2)]N(R2).sub.2, N(R2)N(R2)CO.sub.nR2,
NR2PO.sub.nN(R2).sub.2, NR2PO.sub.nOR2, OC(O)R2, OC(S)R2,
OC(O)N(R2).sub.2, OC(S)N(R2).sub.2, OPO.sub.n(R2).sub.2.
[0242] Preferably, R7 is C(O).sub.nR8; provided that when n=2; R8
is not H; C(S)R8, C(O)N(R8).sub.2, C(S)N(R8).sub.2, S(O).sub.nR8,
S(O)nN(R8).sub.2.
[0243] Preferably, R8 is R2, R3, or R6; and Z is N, O, or S.
[0244] FIG. 7 describes a set of three-dimensionally-conserved
substructures of an HIV protease substrate binding site and the
substructure of atoms of an inhibitor interacting with the
conserved substructure of the protease. The substructures are
defined by the set of atomic coordinates, referred to an orthogonal
system of coordinates shown below. The skilled artisan will
recognize that any set of coordinates derived by applying arbitrary
rotations and translations to the set of atomic coordinates in this
table will be equivalent to the coordinates shown. The values of
the coordinates (x,y,z) of the atoms defining the substructure are
affected by a standard error .sigma.. Therefore (x,y,z) values for
each atom are those defined in the intervals (x-.sigma., x+.sigma.)
for coordinate x, (y-.sigma., y+.sigma.) for coordinate y, and
(z-.sigma., z+.sigma.) for coordinate z.
[0245] Accordingly, the invention provides an HIV protease
inhibitor having the formula I: X-A-B-A'-X' I
[0246] wherein X is a moiety comprising first and second hydrogen
bond acceptor atoms H.sub.A1:X and H.sub.A2:X, wherein H.sub.A1:X
forms a hydrogen bond with N29 of HIV protease and H.sub.A2:X forms
a hydrogen bond with N30 of HIV protease at the relative positions
designated in Table 8;
[0247] wherein A is an optionally substituted linker moiety
comprising a linear chain of 2-6 atoms, wherein A comprises a
hydrogen bond acceptor atom H.sub.A:A, and a hydrogen bond donor
atom H.sub.D:A, and wherein H.sub.A:A forms a hydrogen bond with
solvated water301 of said protease at a relative position
designated by O301, and HD:A forms a hydrogen bond with the
backbone CO atom of residue 27 of said protease at a relative
position designated by O27;
[0248] wherein B comprises a hydrogen bond donor or acceptor atom
H.sub.D/A:B, wherein H.sub.D/A:B forms a hydrogen bond with either
or both carboxylate side chain oxygens of Asp25 and Asp 125 of said
protease at relative positions designated by OD1 25, OD2 25, OD1
125, and OD2 125;
[0249] wherein A' is an optionally substituted linker moiety
comprising a linear chain of 2-6 atoms, comprising a hydrogen bond
acceptor atom H.sub.A:A', wherein H.sub.A:A' forms a hydrogen bond
with solvated water301 of said protease at a relative position
designated by O301; and
[0250] wherein X' is a moiety comprising a hydrogen bond acceptor
atom H.sub.A:X', wherein H.sub.A:X' forms a hydrogen bond with
backbone NH atoms of residues 129 and/or 130 of said protease at
relative positions designated by N129 and/or N130.
[0251] Compound of Formula I is not any of the compounds described
in J. Med. Chem. 39:3278-3290 (1996), in Bioorg. Med. Chem. Lett.
8:687-690 (1998), or Bioorg. Med. Chem. Lett. 8:979-982 (1998).
[0252] In another preferred embodiment, the invention also provides
compounds of the instant invention bound in a complex with wild
type or drug resistant mutant forms of HIV-1 protease.
[0253] In another preferred embodiment, the invention also provides
a composition comprising an inhibitor according to to the instant
invention and a pharmaceutically acceptable additive, excipient, or
diluent.
[0254] In another preferred embodiment, the invention also provides
an pharmaceutical composition comprising an inhibitor according to
the instant invention and another antiretroviral agent.
[0255] In another preferred embodiment, the invention also provides
a composition comprising an inhibitor according to thew instant
invention and a second HIV inhibitor;
[0256] In another preferred embodiment, the invention also provides
an inhibitor according to the instant invention and an additional
HIV protease inhibitor.
[0257] In another preferred embodiment, the invention also provides
an inhibitor according to the instant invention and an HIV reverse
transcriptase inhibitor.
[0258] In another preferred embodiment, the invention also provides
a method of treating a patient suffering from HIV infection,
comprising administering to said patient a composition according to
the instant invention. Preferably, the patient is suffering from a
multi-drug resistant HIV infection.
[0259] The term "alkyl", alone or in combination with any other
term, refers to a straight-chain or branch-chain saturated
aliphatic hydrocarbon radical containing the specified number of
carbon atoms, or where no number is specified, preferably from 1 to
about 15 and more preferably from 1 to about 10 carbon atoms.
Examples of alkyl radicals include, but are not limited to, methyl,
ethyl, n-propyl, isopropyl, n-butyl, isobutyl, sec-butyl,
tert-butyl, pentyl, isoamyl, n-hexyl and the like.
[0260] The term "alkenyl", alone or in combination with any other
term, refers to a straight-chain or branched-chain mono- or
poly-unsaturated aliphatic hydrocarbon radical containing the
specified number of carbon atoms, or where no number is specified,
preferably from 2-10 carbon atoms and more preferably, from 2-6
carbon atoms. Examples of alkenyl radicals include, but are not
limited to, ethenyl, E- and Z-propenyl, isopropenyl, E- and
Z-butenyl, E- and Z-isobutenyl, E- and Z-pentenyl, E- and
Z-hexenyl, E,E-, E,Z-, Z,E- and Z,Z-hexadienyl and the like.
[0261] The term "alkynyl," alone or in combination with any other
term, refers to a straight-chain or branched-chain hydrocarbon
radical having one or more triple bonds containing the specified
number of carbon atoms, or where no number is specified, preferably
from 2 to about 10 carbon atoms. Examples of alkynyl radicals
include, but are not limited to, ethynyl, propynyl, propargyl,
butynyl, pentynyl and the like.
[0262] The term "alkoxy" refers to an alkyl ether radical, wherein
the term "alkyl" is defined above. Examples of suitable alkyl ether
radicals include, but are not limited to, methoxy, ethoxy,
n-propoxy, isopropoxy, n-butoxy, isobutoxy, sec-butoxy, tert-butoxy
and the like.
[0263] The term "aryl," alone or in combination with any other
term, refers to a carbocyclic aromatic radical (such as phenyl or
naphthyl) containing the specified number of carbon atoms,
preferably from 6-15 carbon atoms, and more preferably from 6-10
carbon atoms, optionally substituted with one or more substituents
selected from alkyl, alkoxy, (for example methoxy), nitro, halogen,
(for example chloro), amino, carboxylate and hydroxy. Examples of
aryl radicals include, but are not limited to phenyl, p-tolyl,
4-hydroxyphenyl, 1-naphthyl, 2-naphthyl, indenyl, indanyl,
azulenyl, fluorenyl, anthracenyl and the like.
[0264] The term "aralkyl", alone or in combination, means an alkyl
radical as defined above in which one hydrogen atom is phenyl,
benzyl, 2-phenylethyl and the like.
[0265] The term "aralkoxy carbonyl", alone or in combination, means
a radical of the formula --C(O)--O-aralkyl in which the term
"aralkyl" has the significance given above. An example of an
aralkoxycarbonyl radical is benzyloxycarbonyl.
[0266] The term "aryloxy", alone or in combination, means a radical
of the formula aryl-O-- in which the term "aryl" has the
significance given above.
[0267] The term "alkanoyl", alone or in combination, means an acyl
radical derived from an alkanecarboxylic acid, examples of which
include acetyl, propionyl, butyryl, valeryl, 4-methylvaleryl, and
the like.
[0268] The term "aryloxyalkanoyl" means an acyl radical of the
formula aryl-O-alkanoyl wherein aryl and alkanoyl have the
significance given above.
[0269] The term "aralkanoyl" means an acyl radical derived from an
aryl-substituted alkanecarboxylic acid such as phenylacetyl,
3-phenylpropionyl (hydrocinnamoyl), 4-phenylbutyryl,
(2-naphthyl)acetyl, 4-chlorohydrocinnamoyl, 4-aminohydrocinnamoyl,
4-phenylbutyryl, (1-naphthyl)acetyl, 4-chlorohydrocinnamoyl,
4-aminohydrocinnamoyl, 4-methoxyhydrocinnamoyl, and the like.
[0270] The term "aroyl" means an acyl radical derived from an
aromatic carboxylic acid. Examples of such radicals include
aromatic carboxylic acids, an optionally substituted benzoic or
naphthoic acid such as benzoyl, 4-chlorobenzoyl, 4-carboxybenzoyl,
4-benzyloxycarbonyl)benzoyl, 1-naphthoyl, 2-naphthoyl,
6-carboxy-2-naphthoyl, 6-(benzyloxycarbonyl)-2-naphthoyl,
3-benzyloxy-2-naphthoyl, 3-hydroxy-2-naphthoyl,
3-(benzyloxyformamido)-2-naphthoyl, and the like.
[0271] The term "aminocarbonyl" alone or in combination, means an
amino-substituted carbonyl (carbamoyl) group derived from an
amino-substituted carboxylic acid wherein the amino group can be a
primary, secondary or tertiary amino group continuing substituents
selected from hydrogen, alkyl, aryl, aralkyl, cycloalkyl,
cycloalkylalkyl radicals and the like.
[0272] The term "aminoalkanoyl" means an acyl radical derived from
an amino substituted alkanecarboxylic acid wherein the amino group
can be a primary, secondary or tertiary amino group containing
substituents selected from the group consisting of hydrogen,
cycloalkyl, cycloalkylalkyl radicals and the like, examples of
which include N,N-dimethylaminoacetyl and N-benzylaminoacetyl.
[0273] The term "carbocycle" refers to a non-aromatic stable 3- to
8-membered carbon ring which may be saturated, mono-unsaturated or
poly-unsaturated. The carbocycle may be attached at any endocyclic
carbon atom which results in a stable structure. Preferred
carbocycles have 5-7 carbons.
[0274] The term "cycloalkyl", alone or in combination, means an
alkyl radical which contains from about 3 to about 8 carbon atoms
and is cyclic. Examples of such cycloalkyl radicals include
cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl and the like.
[0275] The term "cycloalkylalkyl" means an alkyl radical as defined
above which is substituted by a cycloalkyl radical containing from
about 3 to about 8, preferably from about 3 to about 6, carbon
atoms.
[0276] The term "cycloalkylcarbonyl" means an acyl group derived
from a monocyclic or bridged cycloalkanecarboxylic acid such as
cyclopropanecarbonyl, cyclohexanecarbonyl, adamantanecarbonyl, and
the like, or from a benz-fused monocyclic cycloalkanecarboxylic
acid which is optionally substituted by, for example,
alkanoylamino, such as 1,2,3,4-tetrahydro-2-naphthoyl,
2-acetamido-1,2,3,4-tetrahydro-2-naphthoyl.
[0277] The term "cycloalkylalkoxycarbonyl" means an acyl group
derived from a cycloalkylalkoxycarboxylic acid of the formula
cycloalkylalkyl-O--COOH wherein cycloalkylalkyl has the
significance given above.
[0278] The term "heterocyclyl" or "heterocycle" refers to a stable
3-7 membered monocyclic heterocyclic ring or 8-11 membered bicyclic
heterocyclic ring which is either saturated or partially
unsaturated, and which may be optionally benzofused if monocyclic
and which is optionally substituted on one or more carbon atoms by
halogen alkyl, alkoxy, oxo, and the like, and/or on a secondary
nitrogen atom (i.e., --NH--) by alkyl, aralkoxycarbonyl, alkanoyl,
phenyl or phenylalkyl or on a tertiary nitrogen atom (i.e., +N--)
by oxido and which is attached via a carbon atom. Each heterocycle
consists of one or more carbon atoms and from one to four
heteroatoms selected from the group consisting of nitrogen, oxygen
and sulfur. As used herein, the terms "nitrogen and sulfur
heteroatoms" include any oxidized form of nitrogen and sulfur, and
the quaternized form of any basic nitrogen. A heterocyclyl radical
may be attached at any endocyclic carbon or heteroatom which
results in the creation of a stable structure. Preferred
heterocycles include 5-7 membered monocyclic heterocycles and 8-10
membered bicyclic heterocycles. Examples of such groups
imidazolinoyl, imidazolidinyl, indazolinolyl, perhydropyridazyl,
pyrrolinyl, pyrrolidinyl, piperidinyl, pyrazolinyl, piperazinyl,
morpholinyl, thiamorpholinyl, thiazolidinyl, thiamorpholinyl
sulfone, oxopiperidinyl, oxopyrrolidinyl, oxoazepinyl,
tetrahydropyranyl, tetrahydrofuranyl, dioxolyl, dioxinyl,
benzodioxolyl, dithiolyl, tetrahydrothienyl, sulfolanyl, dioxanyl,
dioxolanyl, tetahydrofurodihydrofuranyl,
tetrahydropyranodihydrofuranyl, dihydropyranyl,
tetradyrofurofuranyl and tetrahydropyranofuranyl.
[0279] The term heteroaryl refers to a stable 5-6 membered
monocyclic or 8-11 membered bicyclic aromatic heterocycles where
heterocycles is as defined above. Examples of such groups include
imidazolyl, quinolyl, isoqinolyl, indolyl, indazolyl, pyridazyl,
pyridyl, pyrrolyl, pyrazolyl, pyrazinyl, quinoxolyl, pyranyl,
pyrimidinyl, furyl, thienyl, triazolyl, thiazolyl, carbolinyl,
tetrazolyl, benzofuranoyl, thiamorpholinyl sulfone, oxazolyl,
benzoxazolyl, benzimidazolyl, benzthiazolyl, oxopiperidinyl,
oxopyrrolidinyl, oxoazepinyl, azepinyl, isoxozolyl, isothiazolyl,
furazanyl, thiazolyl, thiadiazoyl, oxathiolyl.
[0280] The term "heterocyclylalkanoyl" is an acyl radical derived
from a heterocyclyl-substituted alkane carboxylic acid wherein
heterocyclyl has the significance given above.
[0281] The term "heterocyclyloxycarbonyl" means an acyl group
derived from heterocyclyl-O--COOH wherein heterocyclyl is as
defined above.
[0282] The term "heterocyclylalkoxycarbonyl" means an acyl radical
derived from heterocyclyl-substituted alkane-O--COOH wherein
heterocyclyl has the significance given above.
[0283] The term "heteroaryloxycarbonyl" means an acylradical
derived from a carboxylic acid represented by heteroaryl-O--COOH
wherein heteroaryl has the significance given above.
[0284] The term "halogen" means fluorine, chlorine, bromine or
iodine.
[0285] The term haloalkyl means an alkyl with one or more of its
hydrogens replaced by halogens.
[0286] The term "thioalkyl" means an alkyl radical having at least
one sulfur atom, wherein alkyl has the significance given above. An
example of a thioalkyl is CH.sub.3SCH.sub.3. The corresponding
sulfoxide and sulfone of this thioalkyl CH.sub.3S(O)CH.sub.3 and
CH.sub.3S(O).sub.2CH.sub.3 respectively. Unless expressly stated to
the contrary, the terms "--SO.sub.2-" and "--S(O).sub.2-" as used
herein refer to a sulfone or sulfone derivative (i.e., both
appended groups linked to the S), and not a sulfinate ester.
[0287] The term "substituted", whether preceded by the term
"optionally" or not, and substitutions contained in formulas of
this invention, refer to the replacement of one or more hydrogen
radicals in a given structure with the radical of a specified
substituent. When more than one position in a given structure may
be substituted with more than one substituent selected from a
specified group, the substituents may be either the same or
different at every position (for example, the moiety --N(R2)(R2)).
Typically, when a structure may be optionally substituted, 0-3
substitutions are preferred, and 0-1 substitutions is more
preferred. Most preferred substituents are those which enhance
protease inhibitory activity or intracellular antiviral activity in
permissive mammalian cells or immortalized mammalian cell lines, or
which enhance deliverability by enhancing solubility
characteristics or enhancing pharmacokinetic or pharmacodynamic
profiles as compared to the unsubstituted compound. Combinations of
substituents and variables envisioned by this invention are only
those that result in the formation of stable compounds. The term
"stable", as used herein, refers to compounds which possess
stability sufficient to allow manufacture and administration to a
mammal by methods known in the art. Typically, such compounds are
stable at a temperature of 40.degree. C. or less, in the absence of
moisture or other chemically reactive conditions, for at least a
week.
[0288] This invention also envisions the quaternization of any
basic nitrogen-containing groups of the compounds disclosed herein.
The basic nitrogen can be quaternized with any agents known to
those of ordinary skill in the art including, for example, lower
alkyl halides, such as methyl, ethyl, propyl and butyl chloride,
bromides and iodides; dialkyl sulfates including dimethyl, diethyl,
dibutyl and diamyl sulfates; long chain halides such as decyl,
lauryl, myristyl and stearyl chlorides, bromides and iodides; and
aralkyl halides including benzyl and phenethyl bromides. Water or
oil-soluble or dispersible products may be obtained by such
quaternization.
[0289] As used herein, the compounds of this invention, including
the compounds of formula I are defined to include pharmaceutically
acceptable derivatives or prodrugs thereof. A "pharmaceutically
acceptable derivative or prodrug" means any pharmaceutically
acceptable salt, ester, salt of an ester, or other derivative of a
compound of this invention which, upon administration to a
recipient, is capable of providing (directly or indirectly) a
compound of this invention or an inhibitorily active metabolite or
residue thereof. Particularly favored derivatives and prodrugs are
those that increase the bioavailability of the compounds of this
invention when such compounds are administered to a mammal (e.g.,
by allowing an orally administered compound to be more readily
absorbed into the blood) or which enhance delivery of the parent
compound to a biological compartment (e.g., the brain or lymphatic
system) relative to the parent species.
[0290] Salts derived from appropriate bases include alkali metal
(e.g., sodium), alkaline earth metal (e.g., magnesium), ammonium
and N--(C.sub.1-4alkyl).sub.4.sup.+ salts.
[0291] The compounds of this invention contain one or more
asymmetric carbon atoms and thus occur as racemates and racemic
mixtures, single enantiomers, diastereomeric mixtures and
individual diastereomers. All such isomeric forms of these
compounds are expressly included in the present invention. Each
stereogenic carbon may be of the R or S configuration. Although the
specific compounds exemplified in this application may be depicted
in a particular stereochemical configuration, compounds having
either the opposite stereochemistry at any given chiral center or
mixtures thereof are also envisioned.
[0292] The compounds of the present invention may be used in the
form of pharmaceutically acceptable salts derived from inorganic or
organic acids. Included among such acid salts, for example, are the
following: acetate, adipate, alginate, aspartate, benzoate,
benzenesulfonate, bisulfate, butyrate, citrate, camphorate,
camphorsulfonate, cyclopentanepropionate, digluconate,
dodecylsulfate, ethanesulfonate, fumarate, glucoheptanoate,
glycerophosphate, hemisulfate, heptanoate, hexanoate,
hydrochloride, hydrobromide, hydroiodide, 2-hydroxyethanesulfonate,
lactate, maleate, methanesulfonate, 2-naphthalenesulfonate,
nicotinate, oxalate, pamoate, pectinate, persulfate,
3-phenylpropionate, picrate, pivalate, propionate, succinate,
tartrate, thiocyanate, tosylate and undecanoate.
[0293] The instant compounds may be easily prepared according to
those synthetic methods set forth in U.S. Pat. No. 6,319,946 to
Hale et al., the disclosure of which is incorporated herein by
reference in its entirety. These methods will be evident to those
of ordinary skill in the art.
[0294] The following scheme may be followed to synthesize the
instant compounds where the X substituent can be being varied. In
this scheme P is a standard amine protecting group such as Boc or
Cbz. The amine is reacted with the epoxide as described previously
(J. Med. Chem. 36, 288-291 (93)). The resulting aminoalcohol is
reacted with an activated sulfonic acid derivative where X is a
leaving group such as halo, an activated alcohol, or a sulfonate.
The protecting group is then removed from 3 and the resulting amino
alcohol 4 is reacted with an activated oxycarbonyl derivative 5
(where Y is a leaving group such as halo or an activated alcohol)
to give target compound 6. Compound 5 is generated from the
corresponding alcohol by reacting with an acid chloride or an
activated ester under standard conditions and is either isolated or
used in situ. ##STR25##
[0295] A diprotected amino epoxide such as (N,N-dibenzyl) may also
be used as can an azido group that will eventually be reduced to an
amine. In certain examples the activated sulfonyl derivative may be
reacted with the amine and the resulting sulfonamide reacted with
the epoxide under basic conditions.
[0296] A second representative synthesis can be used when exploring
variations of X'. Here instead of being sulfonylated, amino alcohol
2 can be N-protected by a group that is not removed by removing P,
for example P is Boc and P' is Carbobenzyloxy. The di-protected 7
is then deprotected to give 8 which is reacted as above to give 9.
Following deprotection of 9 various X' groups may be introduced via
the activated sulfonyl derivatives in a similar fashion as
described above. ##STR26## ##STR27##
[0297] An example of a synthesis of X with a third fused ring is
shown below. This olefinic tricyclic system has already been
described by McElvain, et al. JACS 77, 5601 (1955).
Anti-Markownikov addition of water across the double bond using
standard conditions can provide the target alcohol. It is
noteworthy that these authors showed that the unsubstituted
tricyclic system had unusual acid stability, which may help prolong
the activity of our target compounds. ##STR28##
[0298] The synthesis of a bicyclo[2.2.0] system can proceed in a
similar fashion as has been described Padias, et al. J.O.C 52, 5305
(1987) for a homologous analog. R can either be H or a protecting
group such as benzyl that can subsequently be removed under
standard conditions. Protic (e.g. toluenesulfonic) or Lewis (e.g.
scandium triflate) acids can be used for the condensation.
##STR29##
[0299] The synthesis of a representative phosphorus containing
bicycle described herein. Similar chemistry has been described by
Arnold, et al. In Ang. Chem 70, 539 (1958) and Dankiewicz, et al.
in JACS 101, 7712 (1979). The R group in the target shown may
either be H or a protecting group such as benzyl that can
subsequently be removed. ##STR30##
[0300] Other pharmaceutically acceptable salts include a salt with
an inorganic base, organic base, inorganic acid, organic acid, or
basic or acidic amino acid. Inorganic bases which form the instant
pharmaceutically acceptable salts include alkali metals such as
sodium or potassium, alkali earth metals such as calcium and
magnesium or aluminum, and ammonia. Organic bases which form the
instant pharmaceutically acceptable salts include trimethylamine,
triethylamine, pyridine, picoline, ethanolamine, diethanolamine,
triethanolamine, dicyclohexylamine. Inorganic acids which form the
instant pharmaceutically acceptable salts include hydrochloric
acid, hydroboric acid, nitric acid, sulfuric acid, and phosphoric
acid. Organic acids appropriate to form the salt include formic
acid, acetic acid, trifluoroacetic acid, fumaric acid, oxalic acid,
tartaric acid, maleic acid, citric acid, succinic acid, malic acid,
methanesulfonic acid, benzenesulfonic acid, and p-toluenesulfonic
acid. Basic amino acids to form the salt include arginine, lysine
and ornithine. Acidic amino acids to form the salt include aspartic
acid and glutamic acid.
[0301] The instant invention also contemplates compositions which
can be administered orally or non-orally in the form of, for
example, granules, powders, tablets, capsules, syrup,
suppositories, injections, emulsions, elixir, suspensions or
solutions, by mixing these effective components, individually or
simultaneously, with pharmaceutically acceptable carriers,
excipients, binders, diluents or the like.
[0302] The compounds of the present invention-are useful in the
treatment of individuals infected by HIV and for the prophylaxis of
these individuals. The present invention may be useful in the
treatment of mammals infected with viruses whose existence is
mediated by, or depends upon, the protease enzyme. Conditions which
may be prevented or treated with the compourds of the present
invention, especially conditions associated with HIV and other
pathogenic retroviruses, include AIDS, AIDS-related complex (ARC),
progressive generalized lymphadenopathy (POL), as well as chronic
CNS diseases caused by retroviruses, such as, for example
HIV-mediated dementia and multiple sclerosis.
[0303] As a solid formulation for oral administration, the instant
composition may be in the form of powders, granules, tablets, pills
and capsules. In these cases, the instant compounds can be mixed
with at least one additive, for example, sucrose, lactose,
cellulose sugar, mannitol, maltitol, dextran, starch, agar,
alginates, chitins, chitosans, pectins, tragacanth gum, gum arabic,
gelatins, collagens, casein, albumin, synthetic or semi-synthetic
polymers or glycerides. These formulations can contain, as in
conventional cases, further additives, for example, an inactive
diluent, a lubricant such as magnesium stearate, a preservative
such as paraben or sorbic acid, an anti-oxidant such as ascorbic
acid, tocopherol or cysteine, a disintegrator, a binder, a
thickening agent, a buffer, a sweetener, a flavoring agent and a
perfuming agent. Tablets and pills can further be prepared with
enteric coating.
[0304] As used herein, "non-orally" includes subcutaneous
injection, intravenous injection, intramuscular injections,
intraperitoneal injection or instillation. Injectable preparations,
for example, sterile injectable aqueous suspensions or oil
suspensions can be prepared by known procedures in the fields
concerned, using a suitable dispersant or wetting agent and
suspending agent. The sterile injections may be, for example, a
solution or a suspension, which is prepared with a non-toxic
diluent administrable non-orally, such as an aqueous solution, or
with a solvent employable for sterile injection. Examples of usable
vehicles or acceptable solvents include water, Ringer's solution
and an isotonic aqueous saline solution. Further, a sterile
non-volatile oil can usually be employed as solvent or suspending
agent. A non-volatile oil and a fatty acid can be used for this
purpose, including natural or synthetic or semi-synthetic fatty
acid oil or fatty acid, and natural or synthetic mono- or di- or
tri-glycerides.
[0305] The instant pharmaceutical compositions may be formulated
for nasal aerosol or inhalation and may be prepared as solutions in
saline, and benzyl alcohol or other suitable preservatives,
absorption promoters, fluorocarbons, or solubilizing or dispersing
agents.
[0306] Rectal suppositories can be prepared by mixing the drug with
a suitable vehicle, for example, cocoa butter and polyethylene
glycol, which is in the solid state at ordinary temperatures, in
the liquid state at temperatures in intestinal tubes and melts to
release the drug.
[0307] Examples of liquid preparations for oral administration
include pharmaceutically acceptable emulsions, syrups, elixirs,
suspensions and solutions, which may contain an inactive diluent,
for example, water.
[0308] The pharmaceutical composition may be easily formulated for
topical administration with a suitable ointment containing one or
more of the instant compounds suspended or dissolved in a carrier,
which include, mineral oil, liquid petroleum, white petroleum,
propylene glycol, polyoxyethylene polyoxypropylene compound,
emulsifying wax and water. In addition, topical formulations can be
formulated with a lotion or cream containing the active compound
suspended or dissolved in a carrier. Suitable carriers include
mineral oil, sorbitan monostearate, polysorbate 60, cetyl esters
wax, cetearyl alcohol, 2-octyldodecanol, benzyl alcohol and
water.
[0309] Dosages of the instant compounds are dependent on age, body
weight, general health conditions, sex, diet, dose interval,
administration routes, excretion rate, combinations of drugs and
conditions of the diseases treated, while taking these and other
necessary factors into consideration. Generally, dosage levels of
between about 10 .mu.g per day to about 5000 mg per day, preferably
between about 100 mg per day to about 1000 mg per day of the
compound are useful in the prevention and treatment of viral
infection, including HIV infection. Typically, the pharmaceutical
compositions of this invention will be administered from about 1 to
about 5 times per day or alternatively, as a continuous infusion.
Such administration can be used as a chronic or acute therapy.
[0310] The amount of active ingredient that may be combined with
the carrier materials to produce a single dosage form will vary
depending upon the host treated and the particular mode of
administration. A typical preparation will contain from about 5% to
about 95% active compound (w/w). Preferably, such preparations
contain from about 20% to about 80% active compound.
[0311] While these dosage ranges can be adjusted by a necessary
unit base for dividing a daily dose, as described above, such doses
are decided depending on the diseases to be treated, conditions of
such diseases, the age, body weight, general health conditions,
sex, diet of the patient then treated, dose intervals,
administration routes, excretion rate, and combinations of drugs,
while taking these and other necessary factors into consideration.
For example, a typical preparation will contain from about 0.05% to
about 95% active compound (w/w). Preferably, such preparations
contain from about 10% to about 80% active compound. The desired
unit dose of the composition of this invention is administered once
or multiple times daily.
[0312] Accordingly, a preferred embodiment the instant invention
also contemplates compositions and formulations comprising one or
more of the instant compounds in combination with one or more other
HIV protease inhibitors, reverse transcriptase inhibitors, or
non-nucleoside reverse transcriptase inhibitors.
[0313] The compounds of this invention may be administered to an
uninfected or HIV-infected patient either as a single agent or in
combination therapy with other anti-viral agents which interfere
with the replication cycle of HIV in order to increase the
therapeutic effect of these compounds. Thus, the present invention
also relates to a compositions comprising a compound of the present
invention, and another antiretroviral compound as a combined
preparation for simultaneous, separate or sequential use in
treatment of retroviral infections, in particular, in the treatment
of infections with multi-drug resistant retroviruses. Thus, to
combat or treat HIV infections, or the infection and disease
associated with HIV infections, such as Acquired Immunodeficiency
Syndrome (ADS) or AIDS Related Complex (ARC), the compounds of this
invention may be co-administered in combination with for instance,
binding inhibitors, such as, for example, dextran sulfate,
suramine, polyanions, soluble CD4, PRO-542, BMS-806; fusion
inhibitors, such as, for example, T20, T1249, 5-helix, D-peptide
ADS-Ji; co-receptor binding inhibitors, such as, for example, AMD
3100, AMD-3465, AMD7049, AMD3451 (Bicyclams), TAK 779;
SHC-C(SCH351125), SHC-D, PRO-140RT inhibitors, such as, for
example, foscarnet and prodrugs; nucleoside RTIs, such as, for
example, AZT, 3TC, DDC, DDI, D4T, Abacavir, FTC, DAPD, dOTC, DPC
817; nucleotide RTIs, such as, for example, PMEA, PMPA (tenofovir);
NNRTIs, such as, for example, nevirapine, delavirdine, efavirenz, 8
and 9-Cl TIBO (tivirapine), loviride, TMC-125, dapivirine, MKC-442,
UC 781, UC 782, Capravirine, DPC 961, DPC963, DPC082, DPC083,
calanolide A, SJ-1366, TSAO, 4''-deaminated TSAO, MV150, MV026048;
RNAse H inhibitors, such as, for example, SPI093V, PD126338; TAT
inhibitors, such as, for example, RO-5-3335, K12, K37; integrase
inhibitors, such as, for example, L 708906, L 731988, S-1360;
protease inhibitors, such as, for example, amprenavir and prodrug
GW908, ritonavir, nelfinavir, saquinavir, indinavir, lopinavir,
palinavir, .BMS 186316, atazanavir, DPC 681, DPC 684, tipranavir,
AG1776, mozenavir, GS3333, KNI-413, KNI-272, L754394, L756425,
LG-71350, PD161374, PD173606, PD177298, PD178390, PD178392, PNU
140135, TMC114 maslinic acid, U-140690; glycosylation inhibitors,
such as, for example, castanospermine, deoxynojirimycine.
[0314] The combination may in some cases provide a synergistic
effect, whereby viral infectivity and its associated symptoms may
be prevented, substantially reduced, or eliminated completely.
[0315] The compounds of the present invention may also be
administered in combination with immunomodulators (e.g.,
bropirimine, anti-human alpha interferon antibody, IL-2, methionine
enkephalin, interferon alpha, HE-2000 and naltrexone) with
antibiotics (e.g., pentamidine isothiorate) cytokines (e.g. Th2),
modulators of cytokines, chemokines or the receptors thereof (e.g.
CCR5) or hormones (e.g. growth hormone) to ameliorate, combat, or
eliminate HIM infection and its symptoms.
[0316] Such combination therapy in different formulations, may be
administered simultaneously, separately or sequentially.
Alternatively, such combination may be administered as a single
formulation, whereby the active ingredients are released from the
formulation simultaneously or separately.
[0317] The compounds of the present invention may also be
administered in combination with modulators of the metabolization
following application of the drug to an individual. These
modulators include compounds that interfere with the metabolization
at cytochromes, such as cytochrome P450. Some modulators inhibit
cytochrome P450. It is known that several isoenzymes exist of
cytocbrome P450, one of which is cytochrome P450 3A4. Ritonavir is
an example of a modulator of inetabolization via cytoclirome P450.
Such combination therapy in different formulations, may be
administered simultaneously, separately or sequentially.
Alternatively, such combination maybe administered as a single
formulation, whereby the active ingredients are released from the
formulation simultaneously or separately. Such modulator may be
administered at the same or different ratio as the compound of the
present invention. Preferably, the weight ratio of such modulator
vs. a compound of the present invention (modulator:compound of the
present invention) is 1:1 or lower, more preferable the ratio is
1:3 or lower, suitably the ratio is 1:10 or lower, more suitably
the ratio is 1:30 or lower.
[0318] In order to enhance the solubility and/or the stability of
the compounds of formula I in pharmaceutical compositions, .alpha.,
.beta., or .gamma. cyclodextrins or their derivatives may be
emplyed. Also co-solvents such as alcohols may improve the
solubility and/or the stability of the compounds of formula I in
pharmaceutical compositions. In the preparation of aqueous
compositions, addition salts of the subject compounds may be more
suitable due to their increased water solubility.
[0319] Appropriate cyclodextrins are .alpha., .beta., or
.gamma.-cyclodextrins (CDs) or ethers and mixed ethers thereof
wherein one or more of the hydroxy groups of the anhydroglucose
units of the cyclodextrin are substituted with C1-C6alkyl, such as
methyl, ethyl or isopropyl, e.g. randomly methylated .beta.-CD;
hydroxy C16 alkyl, particularly hydroxy-ethyl, hydroxypropyl or
hydroxybutyl; carboxy C1-C6alkyl, particularly carboxymethyl or
carboxyethyl; C1-C6alkyl-carbonyl, particularly acetyl; C1-C6
alkyloxycarbonylC1-C6alkyl or carboxyC16alkyloxyC1-C6alkyl,
particularly carboxymethoxypropyl or carboxyethoxypropyl;
C1-C6alkylcarbonyloxyC1-C6alkyl, particularly 2-acetyloxypropyl.
Especially noteworthy as complexants and/or solubilizers are
.beta.-CD, randomly methylated .beta.-CD, 2,6-dimethyl-.beta.-CD,
2.-hydroxyethyl-.beta.-CD, 2-hydroxyethyl-.gamma.-CD,
hydroxy-propyl-.gamma.-CD and (2-carboxymethoxy)propyl-.beta.-CD,
and in particular 2-hydroxy-propyl-.beta.-CD (2-HP-.beta.-CD).
[0320] The term mixed ether denotes cyclodextrin derivatives
wherein at least two cyclodextrin hydroxy groups are etherified
with different groups such as, for example, hydroxy-propyl and
hydroxyethyl.
[0321] The present compounds may be formulated in combination with
a cyclodextrin or a derivative thereof as described in
EP-A-721,331. Although the formulations described therein are with
antifungal active ingredients, they are equally relevant for
formulating compounds of the present invention. The formulations
described therein are particularly suitable for oral administration
and comprise an antifungal as active ingredient, a sufficient
amount of a cyclodextrin or a derivative thereof as a solubilizer,
an aqueous acidic medium as bulk liquid carrier and an alcoholic
co-solvent that greatly simplifies the preparation of the
composition. The formulations may also be rendered more palatable
by adding pharmaceutically acceptable sweeteners and/or favors.
[0322] Other convenient ways to enhance the solubility of the
compounds of the present invention in pharmaceutical compositions
are described in WO 94/05263, WO 98/42318, EP-A-499,299 and WO
97/44014, all incorporated herein by reference.
[0323] More in particular, the present compounds may be formulated
in a pharmaceutical composition comprising a therapeutically
effective amount of particles consisting of a solid dispersion
comprising a compound of formula I, and one or more
pharmaceutically acceptable water-soluble polymers.
[0324] The term "a solid dispersion" defines a system in a solid
state comprising at least two components, wherein one component is
dispersed more or less evenly throughout the other component or
components. When said dispersion of the components is such that the
system is chemically and physically uniform or homogenous
throughout or consists of one phase as defined in thermodynamics,
such a solid dispersion is referred to as "a solid solution". Solid
solutions are prefered physical systems because the components
therein are usually readily bioavailable to the organisms to which
they are administered.
[0325] The term "a solid dispersion" also comprises dispersions
which are less homogenous throughout than solid solutions. Such
dispersions are not chemically and physically uniform throughout or
comprise more than one phase.
[0326] The water-soluble polymer in the particles is conveniently a
polymer that has an apparent viscosity of 1 to 100 mPas when
dissolved in a 2% aqueous solution at 20.degree. C.
[0327] Preferred water-soluble polymers are hydroxypropyl
methylcelluloses (HPMC). HPMC having a methoxy degree of
substitution from about 0.8 to about 2.5 and a hydroxypropyl molar
substitution from about 0.05 to about 3.0 are generally water
soluble. Methoxy degree of substitution refers to the average
number of methyl ether groups present per anhydroglucose unit of
the cellulose molecule. Hydroxypropyl molar substitution refers to
the average number of moles of propylene oxide which have reacted
with each anhydroglucose unit of the cellulose molecule.
[0328] The particles as defined hereinabove can be prepared by
first preparing a solid dispersion of the components, and then
optionally grinding or milling that dispersion. Marious techniques
exist for preparing solid dispersions including melt-extrusion,
spray-drying and solution-evaporation.
[0329] It may further be convenient to formulate the present
compounds in the form of nanoparticles which have a surface
modifier adsorbed on the surface thereof in an amount sufficient to
maintain an effective average particle size of less than 1000 nm.
Useful surface modifiers are believed to include those which
physically adhere to the surface of the antiretroviral agent but do
not chemically bond to the antiretroviral agent.
[0330] Suitable surface modifiers can preferably be selected from
known organic and inorganic pharmaceutical excipients. Such
excipients include various polymers, low molecular weight
oligomers, natural products and surfactants. Preferred surface
modifiers include nonionic and anionic surfactants.
[0331] The present compounds may also be incorporated in
hydrophilic polymers and applied as a film over many small beads,
thus yielding a composition with good bioavailability which can
conveniently be manufactured and which is suitable for preparing
pharmaceutical dosage forms for oral administration. The beads
comprise a central, rounded or spherical core, a coating film of a
hydrophilic polymer and an antiretroviral agent and a seal-coating
polymer layer. Materials suitable for use as cores are
pharmaceutically acceptable and have appropriate dimensions and
firmness. Examples of such materials are polymers, inorganic
substances, organic substances, saccharides and derivatives
thereof. The route of administration may depend on the condition of
the subject, co-medication and the like.
[0332] The instant compounds and compositions retain inhibitory
activity, or potency, over a broad spectrum of related but
non-identical retroviral proteases. Accordingly, in another
preferred embodiment, the instant invention includes methods for
treating or preventing viral infections. Treating or preventing
refers to alleviating or hindering symptoms or effects of a viral
infection in an infected animal, such as a mammal, particularly a
human. Treating includes prophylaxis as well as the treatment of
viral infections or symptoms of viral infections. The instant
methods comprise treating an animal with a therapeutically
effective amount of a compound or composition according to the
instant invention. According to a preferred embodiment, the viral
infection is an HIV infection, preferably an mdrHIV infection.
[0333] Moreover, the instant compounds and compositions are
particularly effective as inhibitors against drug resistant and
mdrHIV strains and multi-drug resistant HIV proteases (mdrPR).
Accordingly, in another preferred embodiment, the instant invention
provides methods for inhibiting HIV protease, particularly drug
resistant and multi-drug resistant HIV proteases (mdrPR), with a
therapeutically effective amount of a compound or composition
according to the instant invention.
[0334] In relation to the above, the instant compounds may be used
in vaccines for protecting individuals against viral, specifically,
mdrHIV infections. As such, the instant compounds may be employed
as protease inhibitors as conventionally used in vaccines. In this
regard, one or more of the instant compounds may be combined with a
pharmaceutically acceptable adjuvant conventionally employed in
vaccines and administered in prophylactically effective amounts to
protect individuals over an extended period time against HIV
infection.
[0335] The present invention also relates to a novel compositions
and a methods for improving the pharmacokinetics of drugs which are
metabolized by cytochrome P450 monooxygenase. In addition, the
present invention relates to a novel composition and a method for
inhibiting retroviral proteases and in particular for inhibiting
human immunodeficiency virus (HIV) protease and a composition and a
method for inhibiting a retroviral infection, in particular an HIV
infection.
[0336] In this connection, the present invention provides a method
of improving the pharmacokinetics of a drug (or a pharmaceutically
acceptable salt thereof) which is metabolized by cytochrome P450
monooxygenase comprising coadministering a compound of the instant
invention or a pharmaceutically acceptable salt thereof. When
administered in combination, the two therapeutic agents can be
formulated as separate compositions which are administered at the
same time or different times, or the two therapeutic agents can be
administered as a single composition.
[0337] Drugs which are metabolized by cytochrome P450 monooxygenase
and which benefit from coadministration with a compound of the
instant invetion include, but are not limited to, ritonavir, the
immunosuppressants cyclosporine, FK-506 and rapamycin, the
chemotherapeutic agents taxol and taxotere, the antibiotic
clarithromycin and the HIV protease inhibitors A-77003, A-80987,
MK-639, saquinavir, VX-478, AG1343, DMP-323, XM-450, BILA 2011 BS,
BILA 1096 BS, BILA 2185 BS, BMS 186,318, LB71262, SC-52151, SC-629
(N,N-dimethylglycyl-N-(2-hyrdoxy-3-(((4-methoxyphenyl)sulphonyl)(2-methyl-
propyl)amino) -1-(phenylmethyl)propyl)-3-methyl-L-valinamide),
KNI-272, CGP 53437, CGP 57813 and U-103017.
[0338] In a preferred embodiment of the present invention, there is
disclosed a method for improving the pharmacokinetics of an HIV
protease inhibitor (or a pharmaceutically acceptable salt thereof)
which is metabolized by cytochrome P450 monooxygenase comprising
coadministering a compound of the instant invention or a
pharmaceutically acceptable salt thereof. Such a combination of a
compound of the instant invention or a pharmaceutically acceptable
salt thereof and an HIV protease inhibitor or a pharmaceutically
acceptable salt thereof which is metabolized by cytochrome P450
monooxygenase is useful for inhibiting HIV protease in humans and
is also useful for inhibition, treatment or prophylaxis of an HIV
infection or AIDS (acquired immune deficiency syndrome) in humans.
When administered in combination, the two therapeutic agents can be
formulated as separate compositions which are administered at the
same time or different times, or the two therapeutic agents can be
administered as a single composition.
[0339] The following examples illustrate further the present
invention but, of course, should not be construed in any way of
limiting its scope.
EXAMPLES
Example 1
[0340] This example describes the antiviral activity, resistance
profile, and selection of resistance mutations for a
resistance-repellent PI (UIC-94003, FIG. 1; also referred to as
compound 1, vide infra). Also described in this example is a
preliminary analysis by computer modeling of the structural basis
of the resistance-repellent properties of 1.
[0341] Compound 1 was originally identified as a potent protease
inhibitor of multidrug drug resistant HIV mutants using a novel
biochemical fitness profiling strategy described in Erickson and
Gulnik, WO 99/67417, which application is included herein in its
entirety. The biochemical resistance profile (Ki,mutant/Ki,wild
type) and biochemical fitness, or vitality, profile
(Ki,mutant/Ki,wild type x (kcat,mutant/Km,mutant)/(kcat,wild
type/Km,wild type) of compound 1 is described in Table 1 in Example
13 (as Compound 32) of Erickson and Gulnik, vide supra. Antiviral
potencies against wild type and multi-drug resistant HIV strains
are described in Table 3 in Example 14 of Erickson and Gulnik, vide
supra. Based on the biochemical fitness and antiviral drug
resistance profiles, it was predicted that drug resistant viruses
containing the characteristic mutations described in Erickson and
Gulnik WO 99/67417 would not emerge from the wild type virus in the
presence of 1. This prediction was largely borne out in the present
example, which provides new data on the selection of mutations
using compound 1, as well as additional biological and structural
data related to the antiviral and resistance-repellent properties
of compound 1. Data from the present example are described in
detail in Yoshimura et al., J. Virol., 76, 1349-1358 (2002).
[0342] In Vitro Drug Sensitivity of HIV-1 Laboratory Isolates to
Compound 1 and Other PIs
[0343] The sensitivities of HIV-1.sub.LAI, HIV-1.sub.Ba-L,
HIV-2.sub.EHO and the primary HIV-1 isolates against various drugs
were determined as previously described with minor modifications
(Shiraska et al., Proc. Natl. Acad. Sci. USA, 92, 2398-2402
(1995)). The antiviral activity of 1 was >10-fold more potent
than any of the five currently available PIs against both
HIV-1.sub.LAI and HIV-1.sub.Ba-L in PHA-PBMC (IC.sub.50: 0.0003
.mu.M) (Table 1).
In Vitro Activity of Compound 1 Against Highly PI-Resistant
Clinical HIV-1 Strains
[0344] Compound 1 was also active against highly cross-resistant
HIV-1 strains derived from AIDS patients who had failed on 9 to 11
anti-HIV-1 drugs (Falloon et al., Clin. Infect. Dis., 30, 313-318
(2000); Yoshimura et al., Proc. Natl. Acad. Sci. USA, 96, 8675-8680
(1999)). These HIV-1 strains contained up to fourteen amino acid
substitutions in the protease-encoding region, and had high-level
resistance to RTV, IDV, NFV and APV (6- to >77-fold), and
moderate-to-high level resistance to SQV (3-31-fold), as compared
to a wild-type clinical strain HIV-1.sub.ERS104pre. In contrast, 1
suppressed the replication of all eight isolates with IC.sub.50
values ranging 0.0005-0.0055 .mu.M (Table 2). While two strains
(strains 1 and 7) were 6- and 8-fold less susceptible to 1, the
IC.sub.50 values remained extremely low, 0.004 and 0.0055 .mu.M,
respectively (Table 2).
[0345] Generation of Compound 1-Resistant HIV-1 In Vitro.
[0346] Selection of HIV-1 variants resistant to Compound 1 and a
structurally-related PI, amprenavir, was performed in vitro by
propagating HIV-1.sub.NL4-3 in MT-2 cells in the presence of
increasing concentrations of drug as described in Yoshimura et al.,
(2002), vide supra. The virus required 32 passages to acquire a
100-fold increase in the highest compound 1 concentration at which
the virus could propagate while it required only 21 passages for
the virus to acquire the same level of resistance against
amprenavir (FIG. 2). For the virus to acquire a 500-fold increase
to compound 1, 46 passages were required, while 31 passages were
required for viral acquisition of the same level of resistance
against APV (FIG. 2).
[0347] Nucleotide sequencing of proviral DNAs from the lysates of
infected cells was used to determine the mutations selected by each
drug. Individual protease sequences and their frequency at each
passage are depicted in FIG. 3. The wild-type protease gene
sequence was seen in 8 of 8 clones derived from HIV-1.sub.NL4-3 at
passage 4 (HIV-1.sub.UIC-P4). An A28S mutation at the active site
of the enzyme was seen early (at passage 15) in 5 of 9 clones of
HIV-1.sub.UIC-P15, and it was subsequently seen consistently at
frequencies of >50% (except 44% for HIV-1.sub.P42), suggesting
that this mutation was critical in conferring resistance to
compound 1. A substitution at residue 50 from Ile to Val, seen in
HIV-1 resistant to APV (8, 26), was also identified at passage 26
and beyond. It appeared that the I50V mutation brought about a
significant change in protease since the virus started to replicate
relatively rapidly in the presence of compound 1 following the
emergence of I50V (FIG. 2). It is noteworthy that these two active
site mutations, A28S and I50V, did not co-exist in any clones
except in 3 clones throughout the selection (FIG. 3). Compensatory,
non-active site mutations that were selected at later passages
included L10F, M46I and A71V.
[0348] Sensitivity of Compound 1-Selected HIV-1 to Various PIs
[0349] Viruses at passage 62 with 2 .mu.M 1 (HIV-1.sub.UIC-P62) and
those at passage 30 with 5 .mu.M APV (HIV-1.sub.APV-P30) were
titrated, and their susceptibilities to 1, APV, and several other
PIs were determined (Table 3). HIV-1.sub.UIC-P62 was highly
resistant to APV and 1 (IC.sub.50 values were 20- and 70-fold
greater than that of HIV-1.sub.NL4-3, respectively). However,
HIV-1.sub.UIC-P62 was as sensitive to RTV and SQV as the parental
HIV-1.sub.NL4-3, while it was moderately resistant to IDV and NFV
(7- and 5-fold increases in IC.sub.50 values, respectively). In
contrast, HIV-1.sub.APV-P30 was highly resistant to all PIs tested
except SQV (Table 3). These data suggest that 1 has significant
advantages compared to APV in terms of the emergence of drug
resistance: (i) the viral acquisition of resistance to 1 is
substantially delayed (FIG. 2); (ii) 1 resistant HIV remains
sensitive to all PIs except APV; and, (iii) in contrast,
APV-resistant virus is highly cross-resistant to all PIs, except
SQV (Table 3).
[0350] Molecular Modeling of Interaction of HIV-1 Protease and
Compound 1
[0351] A structural model of HIV-1 protease complexed with Compound
1 was prepared based on the crystal structures of HIV-1 protease
complexed with APV (Kim et al., J. Amer. Chem. Soc., 117, 1181
(1995)) and with compound 49 (Ghosh et al., J. Med. Chem., 37,
1506-2508). These two structures were chosen because Compound 1 is
closely related in structure to APV, except for the presence of the
P2 bis-THF moiety, which is contained in compound 49. FIG. 4 shows
an optimized molecular model of the protease-1 complex, and
illustrates the locations of amino acid residues where
substitutions were identified in HIV-1.sub.P62. Ile50 is located on
the internal surface of the flap of HIV-1 protease from where its
aliphatic side chain atoms making van der Waals contacts with
inhibitor atoms. Ala28 is located between the conserved catalytic
triad, Asp25-Thr26-Gly27, and two major substrate and inhibitor
binding residues, Asp29 and Asp30, but is not itself directly
involved in binding. Met46 is located on the external surface of
the flap of HIV protease. Ile10, Asn88, and Ala71 are located far
from the active site of the enzyme. These mutations presumably
improve the fitness of active site-containing mutants by exerting
long-range effects on inhibitor or substrate binding, or by some
other compensatory mechanism (Erickson and Burt, (1996) vide supra;
Erickson et al., AIDS, (1999) vide supra).
[0352] The model also showed that, using the bound conformation of
APV for compound 1, the two oxygen atoms of the bis-THF group of
compound 1 could be positioned to form hydrogen bonds with the main
chain amides of Asp29 and Asp30 in a manner similar to that
observed previously for compound 49 (FIG. 5). In the model,
compound 1 does not make any interactions with Ala28 (FIG. 5). This
is consistent with the structure of the APV/protease complex, in
which Ala28 also does not play a direct role in binding.
[0353] The high potency of Compound 1 relative to APV is consistent
with previous studies that have shown an increase in potency when a
THF group is replaced by a fused ring bis-THF moiety (Ghosh et al.,
Bioorg. Med. Chem. Lett., 8, 687-690 (1998); Ghosh et al., (1994),
vide supra). The modeling analysis suggests that the increased
potency appears to stem from the ability of the two,
conformationally-constrained, ring oxygen atoms in the bis-TBF
group to form hydrogen bonds with the the main chain amide hydrogen
atoms of Asp29 and Asp30 in the S2 subsite (FIG. 5). Since the main
chain atoms cannot mutate, these interactions may be important for
1's broad spectrum of activity against multi-drug resistant
variants.
[0354] No amino acid mutations were seen (except at early passages
during the selection of HIV-1 with 1) at the two active site
residues, Val82 and Ile84, whose side chains are involved in making
direct contacts with all PIs. Mutations at these two active sites
are commonly seen in HIV-1 resistant to various PIs. Mutations at
Val82 are highly effective at conferring resistance and, when
combined with a second active site mutation, such as V32I, can
result in widespread biochemical cross-resistance to PIs. The Ile84
residue, along with the symmetry-related I84', makes interactions
across S2/S1' and S1/S2' subsites, respectively, and the I84V
mutation has been observed in clinical resistance with various PIs
including RTV, IDV, SQV, and APV. HIV-1 propagated in the presence
of compound 1 did not attain stable mutations at V82, and did not
acquire those at I84V (except for one clone), indicating that the
acquisition of resistance to this PI by wild type HIV-1 may require
different evolutionary pathways than have been heretofore observed
for most PIs.
[0355] The D30N mutation is a primary resistance mutation for
nelfinavir, which forms a hydrogen bond with the side chain of
Asp30). and has no effect on binding of compound 1. Consistent with
these observations, HIV-1 exposed to 1 does not select mutations at
codon 30.
[0356] Infectious clones containing either A28S or I50V in the
pNL4-3 background replicated poorly compared to HIV-1 wt in MT-2
cells (data not shown). In a published biochemical study, the A28S
mutation in HIV protease caused a more than 1,500-fold decrease in
K.sub.cat/K.sub.m values for peptide substrates (Hong, et al.,
Protein Sci., 7, 300-305 (1998)). These results suggest that, while
the A28S mutation represents a critical mutation for resistance to
1, it confers a severe replication disadvantage on the virus.
[0357] When HIV-1.sub.NL4-3 was propagated in the presence of
increasing concentrations of 1 or APV, the appearance of HIV-1
strains that were highly resistant to 1 were delayed compared to
the appearance of HIV-1 strains highly resistant to APV (FIG. 2).
Taken together, the above data are consistent with the prediction
that compound 1 is a "resistance-repellent" PI as defined
above.
[0358] These data suggest that 1 and other compounds having the
general structure described herein have at least four advantages:
(i) they exert potent activity against a wide spectrum of
drug-resistant HIV-1 variants presumably due to their interaction
with the main chains of the active site amino acids (Asp29 and
Asp30); and (ii) their unique contact with HIV-1 protease is
different from that of other PIs; (iii) the viral acquisition of
resistance is substantially delayed; and (iv) at least several PIs
remain active in vitro against the virus selected in vitro with 1
or the other compounds (Table 3).
Example 2
[0359] This example illustrates the method by which
experimentally-determined crystal structures of the same inhibitor
in complex with wild type and mutant species of HIV protease can be
compared and analyzed for the existence of a three-dimensionally
conserved substructure.
[0360] The structures of wild type HIV-1 protease and a mutant,
V82F/I84V, HIV-1 protease, both in complexes with the inhibitor
shown in FIG. 1 were determined using conventional x-ray
crystallography techniques. The structures were analyzed by means
of (a) an overall superposition of the atoms of the protein
structures; and, (b) a study of the distances from polar atoms of
the inhibitors to polar atoms of the protein. This analysis
requires three dimensional atomic coordinates of the protein
structures and of the bound inhibitor.
[0361] The superposition of the protein structures was performed in
a two step process: 1) the distance between all pairs of
corresponding C.alpha. atoms (C.alpha. atom of residue number 1 in
one protein to C.alpha. atom of residue number 1 in the second
protein; C.alpha. atom of residue number 2 in one protein to
C.alpha. atom of residue number 2 in the second protein; and so on)
of the polypeptide chains is minimized by means of a least-square
algorithm; 2) the superposition is refined by minimizing, in an
iterative process, the distances between corresponding C.alpha.
atoms that are closer than a given distance (0.25 .ANG. in this
example), thus eliminating regions of the structures having large
conformational differences to compute the superposition parameters.
The distances between equivalenced C.alpha. atoms after the
minimization procedure are shown in Table 4. TABLE-US-00001 TABLE 4
Distances between equivalent C.alpha. atoms Molecule 1: HIV-1 PR
wt: 1 Molecule 2: HIV-1 PR V82F/I84V mutant: 1 distance Molecule 1
Molecule 2 [.ANG.] CA PRO 1 CA PRO 1 0.455 CA GLN 2 CA GLN 2 0.434
CA ILE 3 CA ILE 3 0.418 CA THR 4 CA THR 4 0.317 CA LEU 5 CA LEU 5
0.172 CA TRP 6 CA TRP 6 0.228 CA GLN 7 CA GLN 7 0.364 CA ARG 8 CA
ARG 8 0.166 CA PRO 9 CA PRO 9 0.057 CA LEU 10 CA LEU 10 0.183 CA
VAL 11 CA VAL 11 0.194 CA THR 12 CA THR 12 0.168 CA ILE 13 CA ILE
13 0.146 CA LYS 14 CA LYS 14 0.229 CA ILE 15 CA ILE 15 0.266 CA GLY
16 CA GLY 16 0.662 CA GLY 17 CA GLY 17 0.491 CA GLN 18 CA GLN 18
0.267 CA LEU 19 CA LEU 19 0.112 CA LYS 20 CA LYS 20 0.128 CA GLU 21
CA GLU 21 0.190 CA ALA 22 CA ALA 22 0.169 CA LEU 23 CA LEU 23 0.218
CA LEU 24 CA LEU 24 0.233 CA ASP 25 CA ASP 25 0.160 CA THR 26 CA
THR 26 0.200 CA GLY 27 CA GLY 27 0.303 CA ALA 28 CA ALA 28 0.169 CA
ASP 29 CA ASP 29 0.150 CA ASP 30 CA ASP 30 0.038 CA THR 31 CA THR
31 0.047 CA VAL 32 CA VAL 32 0.173 CA LEU 33 CA LEU 33 0.194 CA GLU
34 CA GLU 34 0.310 CA GLU 35 CA GLU 35 0.260 CA MET 36 CA MET 36
0.136 CA SER 37 CA SER 37 0.494 CA LEU 38 CA LEU 38 0.607 CA PRO 39
CA PRO 39 0.094 CA GLY 40 CA GLY 40 0.774 CA ARG 41 CA ARG 41 0.448
CA TRP 42 CA TRP 42 0.204 CA LYS 43 CA LYS 43 0.596 CA PRO 44 CA
PRO 44 0.625 CA LYS 45 CA LYS 45 0.541 CA MET 46 CA MET 46 0.643 CA
ILE 47 CA ILE 47 0.361 CA GLY 48 CA GLY 48 0.240 CA GLY 49 CA GLY
49 0.182 CA ILE 50 CA ILE 50 0.110 CA GLY 51 CA GLY 51 0.243 CA GLY
52 CA GLY 52 0.200 CA PHE 53 CA PHE 53 0.119 CA ILE 54 CA ILE 54
0.255 CA LYS 55 CA LYS 55 0.295 CA VAL 56 CA VAL 56 0.108 CA ARG 57
CA ARG 57 0.129 CA GLN 58 CA GLN 58 0.074 CA TYR 59 CA TYR 59 0.372
CA ASP 60 CA ASP 60 0.496 CA GLN 61 CA GLN 61 0.780 CA ILE 62 CA
ILE 62 0.406 CA LEU 63 CA LEU 63 0.211 CA ILE 64 CA ILE 64 0.260 CA
GLU 65 CA GLU 65 0.193 CA ILE 66 CA ILE 66 0.181 CA CYS 67 CA CYS
67 0.518 CA GLY 68 CA GLY 68 0.641 CA HIS 69 CA HIS 69 0.319 CA LYS
70 CA LYS 70 0.179 CA ALA 71 CA ALA 71 0.265 CA ILE 72 CA ILE 72
0.350 CA GLY 73 CA GLY 73 0.253 CA THR 74 CA THR 74 0.301 CA VAL 75
CA VAL 75 0.187 CA LEU 76 CA LEU 76 0.186 CA VAL 77 CA VAL 77 0.070
CA GLY 78 CA GLY 78 0.306 CA PRO 79 CA PRO 79 0.047 CA THR 80 CA
THR 80 0.470 CA PRO 81 CA PRO 81 0.404 CA VAL 82 CA PHE 82 0.556 CA
ASN 83 CA ASN 83 0.146 CA ILE 84 CA VAL 84 0.196 CA ILE 85 CA ILE
85 0.163 CA GLY 86 CA GLY 86 0.224 CA ARG 87 CA ARG 87 0.127 CA ASN
88 CA ASN 88 0.048 CA LEU 89 CA LEU 89 0.081 CA LEU 90 CA LEU 90
0.197 CA THR 91 CA THR 91 0.226 CA GLN 92 CA GLN 92 0.176 CA ILE 93
CA ILE 93 0.151 CA GLY 94 CA GLY 94 0.338 CA CYS 95 CA CYS 95 0.233
CA THR 96 CA THR 96 0.305 CA LEU 97 CA LEU 97 0.089 CA ASN 98 CA
ASN 98 0.260 CA PHE 99 CA PHE 99 0.250 CA PRO 101 CA PRO 101 0.227
CA GLN 102 CA GLN 102 0.108 CA ILE 103 CA ILE 103 0.206 CA THR 104
CA THR 104 0.169 CA LEU 105 CA LEU 105 0.125 CA TRP 106 CA TRP 106
0.363 CA GLN 107 CA GLN 107 0.296 CA ARG 108 CA ARG 108 0.400 CA
PRO 109 CA PRO 109 0.173 CA LEU 110 CA LEU 110 0.182 CA VAL 111 CA
VAL 111 0.085 CA THR 112 CA THR 112 0.123 CA ILE 113 CA ILE 113
0.107 CA LYS 114 CA LYS 114 0.368 CA ILE 115 CA ILE 115 0.226 CA
GLY 116 CA GLY 116 0.638 CA GLY 117 CA GLY 117 0.516 CA GLN 118 CA
GLN 118 0.414 CA LEU 119 CA LEU 119 0.102 CA LYS 120 CA LYS 120
0.191 CA GLU 121 CA GLU 121 0.206 CA ALA 122 CA ALA 122 0.197 CA
LEU 123 CA LEU 123 0.231 CA LEU 124 CA LEU 124 0.145 CA ASP 125 CA
ASP 125 0.235 CA THR 126 CA THR 126 0.311 CA GLY 127 CA GLY 127
0.200 CA ALA 128 CA ALA 128 0.102 CA ASP 129 CA ASP 129 0.143 CA
ASP 130 CA ASP 130 0.261 CA THR 131 CA THR 131 0.172 CA VAL 132 CA
VAL 132 0.232 CA LEU 133 CA LEU 133 0.103 CA GLU 134 CA GLU 134
0.175 CA GLU 135 CA GLU 135 0.190 CA MET 136 CA MET 136 0.220 CA
SER 137 CA SER 137 0.739 CA LEU 138 CA LEU 138 0.277 CA PRO 139 CA
PRO 139 0.325 CA GLY 140 CA GLY 140 0.390 CA ARG 141 CA ARG 141
0.174 CA TRP 142 CA TRP 142 0.168 CA LYS 143 CA LYS 143 0.304 CA
PRO 144 CA PRO 144 0.194 CA LYS 145 CA LYS 145 0.456 CA MET 146 CA
MET 146 0.362 CA ILE 147 CA ILE 147 0.178 CA GLY 148 CA GLY 148
0.390 CA GLY 149 CA GLY 149 0.434 CA ILE 150 CA ILE 150 0.050 CA
GLY 151 CA GLY 151 0.199 CA GLY 152 CA GLY 152 0.152 CA PHE 153 CA
PHE 153 0.455 CA ILE 154 CA ILE 154 0.198 CA LYS 155 CA LYS 155
0.470 CA VAL 156 CA VAL 156 0.590 CA ARG 157 CA ARG 157 0.607 CA
GLN 158 CA GLN 158 0.465 CA TYR 159 CA TYR 159 0.301 CA ASP 160 CA
ASP 160 0.294 CA GLN 161 CA GLN 161 0.308 CA ILE 162 CA ILE 162
0.274 CA LEU 163 CA LEU 163 0.235 CA ILE 164 CA ILE 164 0.367 CA
GLU 165 CA GLU 165 0.410 CA ILE 166 CA ILE 166 0.201 CA CYS 167 CA
CYS 167 0.409 CA GLY 168 CA GLY 168 0.406 CA HIS 169 CA HIS 169
0.410 CA LYS 170 CA LYS 170 0.282 CA ALA 171 CA ALA 171 0.273 CA
ILE 172 CA ILE 172 0.317 CA GLY 173 CA GLY 173 0.563 CA THR 174 CA
THR 174 0.129 CA VAL 175 CA VAL 175 0.237 CA LEU 176 CA LEU 176
0.155 CA VAL 177 CA VAL 177 0.240 CA GLY 178 CA GLY 178 0.386 CA
PRO 179 CA PRO 179 0.340 CA THR 180 CA THR 180 0.335 CA PRO 181 CA
PRO 181 0.446 CA VAL 182 CA PHE 182 0.343 CA ASN 183 CA ASN 183
0.205 CA ILE 184 CA VAL 184 0.262 CA ILE 185 CA ILE 185 0.096 CA
GLY 186 CA GLY 186 0.118 CA ARG 187 CA ARG 187 0.202 CA ASN 188 CA
ASN 188 0.073 CA LEU 189 CA LEU 189 0.108 CA LEU 190 CA LEU 190
0.127 CA THR 191 CA THR 191 0.177 CA GLN 192 CA GLN 192 0.175 CA
ILE 193 CA ILE 193 0.241 CA GLY 194 CA GLY 194 0.118 CA CYS 195 CA
CYS 195 0.375 CA THR 196 CA THR 196 0.437 CA LEU 197 CA LEU 197
0.167 CA ASN 198 CA ASN 198 0.178
[0362] Table 4 shows that the I84V, V82F mutations induce
structural changes relative to the wild type structure in some
parts of the enzyme, but that other regions are less affected. The
regions of the protein structure which are not significantly
affected by the amino acid mutations are defined as structurally
conserved regions. In the present example, the mutations result in
localized structural changes in the backbone of HIV protease over a
wide range, from 0.038-0.774 .ANG..
[0363] The distances between the polar atoms of the inhibitor shown
in FIG. 1 to polar atoms of the wild type and mutant protein, that
is hydrogen-bond donors and acceptors, were computed and they are
displayed in Table 5. TABLE-US-00002 TABLE 5 Distances between
polar atoms of the inhibitor and polar atoms of the protein HIV PR
wt: 1 V82F/I84V: 1 O2-Wat301 2.92 2.89 N1-027 3.36 3.46 O6-N30 3.30
3.61 06-N29 3.19 3.55 O7-N29 2.84 2.87 O7-OD1 29 3.42 3.54 O7-O1
3.31 3.19 O3-OD 25 (out) 2.50 2.94 O3-OD 25 (in) 2.65 2.67 O3-OD125
(out) 3.27 3.21 O3-OD125 (in) 2.80 2.67 O5-Wat301 2.70 2.79 O8-N130
3.16 2.96
[0364] Table 5 shows that the polar atoms of the inhibitor interact
with the same polar atoms of the two different proteins, in this
case the wild type and V82F/I84V mutant HIV proteases. From Table
5, it can be seen that the polar atoms of the enzymes with which
the inhibitor interacts belong to the structurally conserved
regions. The effects of mutations on the protein-inhibitor
interactions can be quantified in terms of the distances between
interacting pairs of polar atoms from the inhibitor and from polar
atoms of the three-dimensionally conserved substructure of the
protein. These distances are similar in the wild type and in the
mutant complexes; the average of their differences is only 0.07
.ANG.. The range of the differences is 0.02-0.36 .ANG..
Example 3
[0365] This example illustrates the method by which
experimentally-determined crystal structures of two different
inhibitors in complexes with wild type HIV protease can be compared
and analyzed for the existence of a three-dimensionally conserved
substructure. The structures of wild type HIV-1 protease in
complexes with inhibitor 1 and with Amprenavir (inhibitor 2) were
analyzed by means of (a) an overall superposition of the protein
structures; and (b) a study of the distances from polar atoms of
the inhibitors to polar atoms of the protein.
[0366] The superposition of the protein structures is performed in
a two step process: 1) the distance between all pairs of
corresponding C.alpha. atoms (C.alpha. atom of residue number 1 in
one protein to C.alpha. atom of residue number 1 in the second
protein; C.alpha. atom of residue number 2 in one protein to
C.alpha. atom of residue number 2 in the second protein; and so on)
of the polypeptide chains is minimized by means of a least-square
algorithm; 2) the superposition is refined by minimizing, in an
iterative process, the distances between corresponding C.alpha.
atoms that are closer than a given distance (0.25 .ANG. in this
example), thus eliminating regions of the structures having large
conformational differences to compute the superposition parameters.
The distances between equivalenced C.alpha. atoms after the
minimization procedure are shown in Table 6. TABLE-US-00003 TABLE 6
Distances between equivalent Ca atoms Molecule 1: HIV-1 PR wt: 1
Molecule 2: HIV-1 PR wt: 2 distance Molecule 1 Molecule 2 [.ANG.]
CA PRO 1 CA PRO 1 0.200 CA GLN 2 CA GLN 2 0.320 CA ILE 3 CA ILE 3
0.147 CA THR 4 CA THR 4 0.405 CA LEU 5 CA LEU 5 0.225 CA TRP 6 CA
TRP 6 0.296 CA GLN 7 CA GLN 7 0.317 CA ARG 8 CA ARG 8 0.154 CA PRO
9 CA PRO 9 0.143 CA LEU 10 CA LEU 10 0.259 CA VAL 11 CA VAL 11
0.275 CA THR 12 CA THR 12 0.307 CA ILE 13 CA ILE 13 0.207 CA LYS 14
CA LYS 14 0.273 CA ILE 15 CA ILE 15 0.434 CA GLY 16 CA GLY 16 0.469
CA GLY 17 CA GLY 17 0.414 CA GLN 18 CA GLN 18 0.319 CA LEU 19 CA
LEU 19 0.161 CA LYS 20 CA LYS 20 0.155 CA GLU 21 CA GLU 21 0.196 CA
ALA 22 CA ALA 22 0.338 CA LEU 23 CA LEU 23 0.246 CA LEU 24 CA LEU
24 0.292 CA ASP 25 CA ASP 25 0.142 CA THR 26 CA THR 26 0.109 CA GLY
27 CA GLY 27 0.176 CA ALA 28 CA ALA 28 0.193 CA ASP 29 CA ASP 29
0.087 CA ASP 30 CA ASP 30 0.118 CA THR 31 CA THR 31 0.111 CA VAL 32
CA VAL 32 0.087 CA LEU 33 CA LEU 33 0.306 CA GLU 34 CA GLU 34 0.333
CA GLU 35 CA GLU 35 0.399 CA MET 36 CA MET 36 0.296 CA SER 37 CA
SER 37 0.454 CA LEU 38 CA LEU 38 0.451 CA PRO 39 CA PRO 39 0.397 CA
GLY 40 CA GLY 40 0.444 CA ARG 41 CA ARG 41 0.535 CA TRP 42 CA TRP
42 0.346 CA LYS 43 CA LYS 43 0.442 CA PRO 44 CA PRO 44 0.548 CA LYS
45 CA LYS 45 0.307 CA MET 46 CA MET 46 0.320 CA ILE 47 CA ILE 47
0.403 CA GLY 48 CA GLY 48 0.237 CA GLY 49 CA GLY 49 0.280 CA ILE 50
CA ILE 50 0.206 CA GLY 51 CA GLY 51 0.368 CA GLY 52 CA GLY 52 0.315
CA PHE 53 CA PHE 53 0.378 CA ILE 54 CA ILE 54 0.180 CA LYS 55 CA
LYS 55 0.149 CA VAL 56 CA VAL 56 0.302 CA ARG 57 CA ARG 57 0.098 CA
GLN 58 CA GLN 58 0.219 CA TYR 59 CA TYR 59 0.279 CA ASP 60 CA ASP
60 0.385 CA GLN 61 CA GLN 61 0.431 CA ILE 62 CA ILE 62 0.343 CA LEU
63 CA LEU 63 0.473 CA ILE 64 CA ILE 64 0.344 CA GLU 65 CA GLU 65
0.456 CA ILE 66 CA ILE 66 0.481 CA CYS 67 CA CYS 67 0.920 CA GLY 68
CA GLY 68 0.999 CA HIS 69 CA HIS 69 0.295 CA LYS 70 CA LYS 70 0.406
CA ALA 71 CA ALA 71 0.446 CA ILE 72 CA ILE 72 0.374 CA GLY 73 CA
GLY 73 0.259 CA THR 74 CA THR 74 0.276 CA VAL 75 CA VAL 75 0.165 CA
LEU 76 CA LEU 76 0.220 CA VAL 77 CA VAL 77 0.202 CA GLY 78 CA GLY
78 0.231 CA PRO 79 CA PRO 79 0.131 CA THR 80 CA THR 80 0.374 CA PRO
81 CA PRO 81 0.472 CA VAL 82 CA VAL 82 0.554 CA ASN 83 CA ASN 83
0.149 CA ILE 84 CA ILE 84 0.261 CA ILE 85 CA ILE 85 0.223 CA GLY 86
CA GLY 86 0.130 CA ARG 87 CA ARG 87 0.165 CA ASN 88 CA ASN 88 0.103
CA LEU 89 CA LEU 89 0.072 CA LEU 90 CA LEU 90 0.076 CA THR 91 CA
THR 91 0.114 CA GLN 92 CA GLN 92 0.115 CA ILE 93 CA ILE 93 0.204 CA
GLY 94 CA GLY 94 0.220 CA CYS 95 CA CYS 95 0.068 CA THR 96 CA THR
96 0.185 CA LEU 97 CA LEU 97 0.095 CA ASN 98 CA ASN 98 0.311 CA PHE
99 CA PHE 99 0.216 CA PRO 101 CA PRO 1 0.455 CA GLN 102 CA GLN 2
0.121 CA ILE 103 CA ILE 3 0.120 CA THR 104 CA THR 4 0.109 CA LEU
105 CA LEU 5 0.128 CA TRP 106 CA TRP 6 0.205 CA GLN 107 CA GLN 7
0.229 CA ARG 108 CA ARG 8 0.211 CA PRO 109 CA PRO 9 0.195 CA LEU
110 CA LEU 10 0.135 CA VAL 111 CA VAL 11 0.086 CA THR 112 CA THR 12
0.166 CA ILE 113 CA ILE 13 0.199 CA LYS 114 CA LYS 14 0.333 CA ILE
115 CA ILE 15 0.356 CA GLY 116 CA GLY 16 0.671 CA GLY 117 CA GLY 17
0.709 CA GLN 118 CA GLN 18 0.370 CA LEU 119 CA LEU 19 0.258 CA LYS
120 CA LYS 20 0.156 CA GLU 121 CA GLU 21 0.250 CA ALA 122 CA ALA 22
0.276 CA LEU 123 CA LEU 23 0.103 CA LEU 124 CA LEU 24 0.112 CA ASP
125 CA ASP 25 0.078 CA THR 126 CA THR 26 0.057 CA GLY 127 CA GLY 27
0.121 CA ALA 128 CA ALA 28 0.098 CA ASP 129 CA ASP 29 0.190 CA ASP
130 CA ASP 30 0.302 CA THR 131 CA THR 31 0.073 CA VAL 132 CA VAL 32
0.178 CA LEU 133 CA LEU 33 0.147 CA GLU 134 CA GLU 34 0.239 CA GLU
135 CA GLU 35 0.101 CA MET 136 CA MET 36 0.235 CA SER 137 CA SER 37
0.391 CA LEU 138 CA LEU 38 0.364 CA PRO 139 CA PRO 39 0.532 CA GLY
140 CA GLY 40 0.213 CA ARG 141 CA ARG 41 0.448 CA TRP 142 CA TRP 42
0.133 CA LYS 143 CA LYS 43 0.195 CA PRO 144 CA PRO 44 0.082 CA LYS
145 CA LYS 45 0.359 CA MET 146 CA MET 46 0.306 CA ILE 147 CA ILE 47
0.076 CA GLY 148 CA GLY 48 0.214 CA GLY 149 CA GLY 49 0.205 CA ILE
150 CA ILE 50 0.163 CA GLY 151 CA GLY 51 0.287 CA GLY 152 CA GLY 52
0.318 CA PHE 153 CA PHE 53 0.125 CA ILE 154 CA ILE 54 0.189 CA LYS
155 CA LYS 55 0.384 CA VAL 156 CA VAL 56 0.510 CA ARG 157 CA ARG 57
0.405 CA GLN 158 CA GLN 58 0.139 CA TYR 159 CA TYR 59 0.361 CA ASP
160 CA ASP 60 0.252 CA GLN 161 CA GLN 61 0.414 CA ILE 162 CA ILE 62
0.337 CA LEU 163 CA LEU 63 0.202 CA ILE 164 CA ILE 64 0.359 CA GLU
165 CA GLU 65 0.463 CA ILE 166 CA ILE 66 0.347 CA CYS 167 CA CYS 67
0.256 CA GLY 168 CA GLY 68 0.471 CA HIS 169 CA HIS 69 0.658 CA LYS
170 CA LYS 70 0.489 CA ALA 171 CA ALA 71 0.445 CA ILE 172 CA ILE 72
0.396 CA GLY 173 CA GLY 73 0.523 CA THR 174 CA THR 74 0.130 CA VAL
175 CA VAL 75 0.156 CA LEU 176 CA LEU 76 0.077 CA VAL 177 CA VAL 77
0.129 CA GLY 178 CA GLY 78 0.276 CA PRO 179 CA PRO 79 0.272 CA THR
180 CA THR 80 0.580 CA PRO 181 CA PRO 81 0.436 CA VAL 182 CA VAL 82
0.328 CA ASN 183 CA ASN 83 0.180 CA ILE 184 CA ILE 84 0.151 CA ILE
185 CA ILE 85 0.104 CA GLY 186 CA GLY 86 0.059 CA ARG 187 CA ARG 87
0.058 CA ASN 188 CA ASN 88 0.183 CA LEU 189 CA LEU 89 0.164 CA LEU
190 CA LEU 90 0.051 CA THR 191 CA THR 91 0.216 CA GLN 192 CA GLN 92
0.162 CA ILE 193 CA ILE 93 0.158 CA GLY 194 CA GLY 94 0.047 CA CYS
195 CA CYS 95 0.050 CA THR 196 CA THR 96 0.200 CA LEU 197 CA LEU 97
0.165 CA ASN 198 CA ASN 98 0.074
[0367] The distances between the polar atoms of the inhibitors 1
(FIG. 1) and 2 to polar atoms of the protein, that is,
hydrogen-bond donors and acceptors, were computed and are shown in
Table 7. TABLE-US-00004 TABLE 7 Distances between polar atoms of
inhibitors and polar atoms of the proteins Wt: 1 Wt: 2 complex
complex O2-Wat301 2.92 3.02 N1-027 3.36 3.58 O6-N30 3.30 3.50
06-N29 3.19 3.51 O7-N29 2.84 -- O7-OD1 29 3.42 -- O7-O1 3.31 --
O3-OD 25 2.50 2.80 (out) A O3-OD 25 2.65 2.66 (in) A O3-OD 25 3.27
3.07 (out) B O3-OD 25 2.80 2.68 (in) B O5-Wat301 2.70 2.77 O8-N 30
3.16 -- N3-N 30 3.17 N3-OD2 30 3.15
[0368] Inhibitors 1 (FIG. 1) and 2 (Amprenavir) have similar
structural elements, in particular their core, i.e. groups at the
P1-P1' positions. However, 2 has a THF group while 1 has a bis-THF
group at the P2' position. The P2 groups are identical except for
the substitution of an ether oxygen atom in 1 as compared to an
amine nitrogen atom at the same position in 2. Table 7 shows that 1
forms more polar interactions with the atoms of the protein that
were previously identified as belonging to the structurally
conserved substructure than does compound 2. For example, the O7
oxygen atom in compound 1, that forms a polar interaction with N29
nitrogen of the protease, has no counterpart in compound 2.
Instead, the O6 oxygen atom of 2 forms longer (and presumably
weaker) hydrogen bonds with both N30 (3.50 .ANG.) and N29 (3.51
.ANG.). In contrast, the O6 oxygen of compound 1 forms a shorter
(and presumably stronger) hydrogen bond with N29 (3.19 .ANG.).
Additionally, as can be seen in Table 7, where both compounds 1 and
2 form interactions with polar atoms in the structurally conserved
substructure of HIV protease, the distances between interacting
atoms are consistently shorter for compound 1, indicative of
presumably stronger binding interactions.
Example 4
[0369] Examples 2 and 3 were used to identify a three
dimensionally-conserved substructure of HIV protease that is
involved in the binding of HIV protease inhibitors and, in
particular, to identify polar atoms of these substructural elements
that are involved in forming interactions with polar atoms of HIV
protease inhibitors. The following two examples demonstrate that a
protease inhibitor that contains polar atoms that can make
favorable interactions with the polar atoms of the substructure may
exhibit resistance-repellent properties.
[0370] Compounds 1 and 3 both contain a Bis-THF group at the P2
position that contains two polar atoms, in particular, hydrogen
bond acceptor oxygen atoms, that can form hydrogen bonds with the
two hydrogen atoms attached to the backbone amide nitrogen atoms on
the protein at residues 29 and 30. All three compounds differ in
the P2' substituent. Compounds 1 and 3 both are unaffected by the
two active site mutations, V82F and I84V, and Ki values for wild
type and mutant enzymes are similar for both compounds. In
contrast, compound 2, which contains only a single hydrogen bond
acceptor atom in the P2 substitutent, is dramatically affected by
the active site mutations, which demonstrate high level resistance
to 2.
[0371] The antiviral activity of compounds 1 and 3 against HIV
derived from patient isolates that contain multiple mutations are
equivalent to their activity against wild type HIV strains. In
contrast, compound 2 is much less effective against the same mutant
viruses. None of the patients from whom virus was isolated had ever
been exposed to any of the compounds tested herein. Nonetheless,
compound 2 exhibited cross resistance to these virus strains that
is typically seen with all clinically useful HIV protease
inhibitors--4 (Saquinavir), 5 (Ritonavir), 6 (Indinavir) and 7
(Nelfinavir). Compounds 2, 4, 5, 6, and 7 have very different
chemical structures, but nonetheless behave as a single class with
respect to their antiviral behavior against wild type and multidrug
resistant HIV strains. All compounds are dramatically less potent
against the multidrug resistant strains of HIV.
[0372] In sharp contrast, compounds 1 and 3, which closely resemble
each other as well as compound 2, exhibit resistance-repellent
behavior in that they are equally effective against wild type and
mutant HIV strains that exhibit high level multidrug resistance
towards compounds 2, 4, 5, 6, and 7. The resistance-repellent
activity of compound 1 was completely unexpected and contrasts with
the common and typical loss of antiviral potency experienced with
compounds like 2, 4, 5, 6, 7, and indeed most other HIV protease
inhibitors represented as similar or different structures that have
been reported.
[0373] The development and application of the 3D motif method
described above successfully revealed the presence of a unique,
three dimensionally-conserved substructure of HIV protease that is
useful in the design of resistance-repellent inhibitors. Based on
this method, compound 3 was predicted, on the basis of comparative
molecular modeling using the coordinates of the complexes of
compound 1 with wild type and V82F/I84V mutant HIV proteases, to be
able to make the same key polar interaction as compound 1 and
thereby to exhibit resistance-repellent properties. Based on these
data, it is feasible to design protease inhibitors that are
predicted to have resistance-repellent properties, and are
predicted to be useful for the treatment of both wild type (first
line therapy) and drug resistant (salvage therapy) HIV
infections.
[0374] Any reference to any of the instant compounds also includes
a reference to a pharmaceutically acceptable salts thereof.
[0375] Any reference to any of the instant compounds also includes
a reference to a stereoisomer thereof.
[0376] Other substitutions, modifications, changes and omissions
may be made in the design, operating conditions and arrangement of
the preferred embodiments without departing from the spirit of the
invention as expressed in the appended claims.
[0377] Additional advantages, features and modifications will
readily occur to those skilled in the art. Therefore, the invention
in its broader aspects is not limited to the specific details, and
representative devices, shown and described herein. Accordingly,
various modifications may be made without departing from the spirit
or scope of the general inventive concept as defined by the
appended claims and their equivalents.
[0378] All of the references cited herein, including patents,
patent applications, and publications, are hereby incorporated in
their entireties by reference.
[0379] The claims below are not restricted to the particular
embodiments described above.
* * * * *