Note : Les descriptions sont présentées dans la langue officielle dans laquelle elles ont été soumises.
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ANTIBIOTIC TETRAHYDRO-BETA-CARBOLINE DERIVATIVES
Related Application
This application claims priority to U.S. Provisional Application No.
60/991,520,
Attorney Docket No. NPZ-006-1, filed November 30, 2007, entitled "ANTIBIOTIC
TETRAHYDRO-BETA-CARBOLINE DERIVATIVES." The contents of any patents,
patent applications, and references cited throughout this specification are
hereby
incorporated by reference in their entireties.
Technical Field
The present invention relates to compositions which are PPAT inhibitors and
methods and uses thereof.
Background of the Invention
In the last century, antibiotics were developed that led to significant
reductions in
mortality. Unfortunately, widespread use has led to the rise of antibiotic
resistant
bacteria, e.g., methicillin resistant Staphyloccocus aureus (MRS A),
vancomycin
resistant enterococci (VRE), and penicillin-resistant Streptococcus pneumonias
(PRSP).
Some bacteria are resistant to a range of antibiotics, e.g., strains of
Mycobacterium
tuberculosis resist isoniazid, rifampin, ethambutol, streptomycin,
ethionamide,
kanamycin, and rifabutin. In addition to resistance, global travel has spread
relatively
unknown bacteria from isolated areas to new populations. Furthermore, there is
the
threat of bacteria as biological weapons. These bacteria may not be easily
treated with
existing antibiotics.
Infectious bacteria employ the coenzyme A (CoA) biosynthesis pathway, and,
particularly in the penultimate step of the pathway, depend on
phosphopantetheine
adenyl transferase (PPAT), which transfers an adenyl moiety from adenosine
triphosphate (ATP) to 4'-phosphopanthetheine, forming dephospho-CoA (dPCoA).
While PPAT is present in mammalian cells, bacterial and mammalian PPAT enzymes
differ substantially in primary sequence (about 18% identity) and physical
properties.
Thus, PPAT presents a desirable, selective target for new antibiotics.
Recent efforts have resulted in the identification of compounds that inhibit
E.
coli PPAT (Leslie, et al. "Antibacterial Anthranilates with a Novel Mode of
Action";
Zhao, et al. "Inhibitors of Phosphopantetheine Adenylyltransferase"; Presented
at the
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42nd Interscience Conference on Antimicrobial Agents and Chemotherapy (ICAAC),
San Diego, CA, 2002). However, these compounds are not appropriate for drug
development. Furthermore, in one case, the structures are peptidic, while in
the other
case, representative compounds exhibited poor activity against purified PPAT.
Therefore, there is a need for new antibiotics that target PPAT, whereby
infections from bacteria dependent on PPAT can be treated.
Summary of the Invention
The present invention relates to certain bicyclic PPAT inhibitors. The
disclosed
compounds have antibiotic activity against bacteria, including drug-resistant
bacteria.
Thus, compounds that are PPAT inhibitors, methods of treatment with the
disclosed
PPAT inhibitors, and pharmaceutical compositions comprising the disclosed PPAT
inhibitors are provided herein.
In one aspect, the invention provides a method of treating a subject for a
bacterial
infection, comprising administering to a subject in need of treatment for a
bacterial
infection an effective amount of a compound represented by structural Formula
I:
R6
A R5 R4
N~L-11
R3
(I)
and pharmaceutically acceptable salts, solvates, hydrates, enantiomers,
stereoisomers, rotamers, tautomers, diastereomers, or racemates thereof.
The invention is useful for treating (therapeutically or prophylactically)
bacterial
infections, particularly infections caused by bacteria that depend on the CoA
biosynthesis pathway, and more particularly, infections caused by bacteria
that express
the PPAT enzyme. Furthermore, it is useful against bacteria that have
developed
antibiotic resistance, especially multiple drug resistant strains, because it
is believed to
act through a different mechanism than existing, widely used antibiotics.
DETAILED DESCRIPTION OF THE INVENTION
The invention is generally related to methods, compounds, and pharmaceutical
compositions for treating and preventing bacterial infections. In particular,
the invention
relates to tetrahydro-(3-carboline derivatives that are PPAT inhibitors.
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In a preferred embodiment, the compound is represented by structural Formula
I:
R6
A R5 R4
N~L-11
R3
(I)
and pharmaceutically acceptable salts, solvates, hydrates, enantiomers,
stereoisomers, rotamers, tautomers, diastereomers, or racemates thereof;
wherein
ring A is an aryl or heteroaryl group that is optionally substituted at any
substitutable ring atom;
J is -0-, -5-, or -NR2-, wherein R2 is -H or optionally substituted C1-C5
alkyl;
or, J is -NR2'-, wherein R2' is optionally substituted aryl, aralkyl,
heteroaryl,
heteroaralkyl, C3-C7 cycloaliphatic, or C3-C7 cycloalkyl;
R3 is optionally substituted aryl, aralkyl, heteroaryl, heteroaralkyl, C3-C7
cycloaliphatic, or C3-C7 cycloalkyl;
L is -(CH2)-, -(CO)-, -(CS)-, -(SO)-, or -(SO2)-;
R4 is an aryl, biaryl, heteroaryl, biheteroaryl, heteroaryl-aryl, aryl-
heteroaryl,
aralkyl, heteroaralkyl, C1-C8 aliphatic, C3-C7 cycloalkyl, C5-C7
cycloaliphatic, or a 3-7
membered non-aromatic heterocyclic group;
wherein R4 can be substituted with halogen, -(CO)ORa, -(CO)O(CO)Ra, -
(CS)ORa, -(SO)ORa, S03Ra, -OSO3Ra, -P(ORa)2, -(PO)(ORa)2, -O(PO)(ORa)2, -
B(ORa)2,
-(CO)NRb2, -NRc(CO)Ra, -SO2NRb2, or -NRcSO2Ra;
R5 is -H, -(CO)ORa, -(CO)O(CO)Ra, -(CS)ORa, -(SO)ORa, S03Ra, -OS03Ra, -
P(ORa)2, -(PO)(ORa)2, -O(PO)(ORa)2, -B(ORa)2, -(CO)NRb2, -NRc(CO)Ra, -SO2NRb2,
or
-NRcS02Ra;
R6 is -H, -OH, halogen, or optionally substituted C1-C3 alkyl or alkoxy;
each Ra and Rc are, independently, -H, C1-C5 alkyl, aryl, or aralkyl;
each Rb is, independently, -H, C1-C5 alkyl, aryl, or aralkyl, or NRb2 is a
nonaromatic heterocyclic group.
In one embodiment, ring A in structural Formula I is an optionally substituted
heteroaryl group, for example, an optionally substituted pyrazyl, furanyl,
pyrrolyl,
thienyl, oxazolyl, isooxazolyl, thiazolyl, isothiazolyl, or imidazolyl group.
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Suitable optional substituents for substitutable ring atoms in Ring A are
provided
herein below in the section describing substituents for aryl and heteroaryl
groups. More
preferably, Ring A is optionally, independently, substituted at any
substitutable ring
atom with Rl. Each Rl are, independently, halogen, -CN, -NO2, -CF3, -OCF3, -
ORd, -
(CO)Rd, -(CO)ORd, -O(CO)Rd, -(CO)O(CO)Rd, -(CS)ORd, -(SO)ORd, -SO3Rd, -
CONRe2, O(CO)NRe2, NRf(CO)NRe2, NRf(CO)ORd, -NR' CORd, -(SO2)NRe2, -
NRfSO2Rd, -(CH2),NRd2, or optionally substituted aryl, aralkyl or C1-C5 alkyl.
In the
preceding, s is from 0 to 5, each Rd and Rf are, independently, -H, aryl,
aralkyl, C1-C5
alkyl, or C1-C5 haloalkyl, and each Rc are, independently, -H, aryl, aralkyl,
or C1-C5
alkyl, and NRe2 is a nonaromatic heterocyclic group, for example, piperidinyl,
morpholinyl, and the like. More preferably, R1 is halogen, -CN, -NO2, -CF3, -
OCF3, -
d, -(CO)Rd, -(CO)ORd, -O(CO)Rd, -CONRe2, -O(CO)NRe2, -NRf(CO)ORd
OR , -
NRfCORd, -(SO2)NRe2, -NRfS02Rd, (CH2)SNRd2, or optionally substituted aryl,
aralkyl
or C1-C5 alkyl. Even more preferably, R1 is -H, -OH, -F, -CH3, -CF3, -OCH3 or -
OCF3.
Most preferably, R1 is -H.
In one embodiment, R3 in structural Formula I is an optionally substituted
phenyl, pyridyl, benzo[1,3]dioxolyl, 2,3-dihydro-benzo[1,4]dioxinyl,
pyrimidyl, pyrazyl,
furanyl, pyrrolyl, thienyl, oxazolyl, isooxazolyl, thiazolyl, isothiazolyl,
imidazolyl,
naphthyl, quinolinyl, biphenyl, benzopyrimidyl, benzopyrazyl, benzofuranyl,
indolyl,
benzothienyl, benzoxazolyl, benzoisooxazolyl, benzothiazolyl,
benzoisothiazolyl, or
benzimidazolyl group. Suitable optional substituents for the group represented
by R3
are provided herein below.
More preferably, R3 in structural Formula I is represented by one of
structural
formulas R3-i to R3-v:
O (R1 1)w '0 (R11),,
(R11)"
R3-i R3-ii R3-iii
Z Z
(R11%, (R11)w
(R1 1)w
(R 11),
R3-iv R3-v
In structural formulas R3-i to R3-v, Y is -N-, -CH-, or -CR11-; Z is -NR'-, -5-
,
or -0-, wherein Rz is -H or C1-C3 alkyl, more preferably -H or methyl, or most
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preferably -H; the variable w is 0, 1, 2, or 3; each R11 are, independently,
halogen, -CN,
-NO2, -CF3, -OCF3, -OR', -(CO)R1, -(CO)OR1, -O(CO)R1, -(CO)O(CO)R1, -(CS)OR1, -
(SO)OR1, -S03R1, -CONRm2, -O(CO)NR-2, -NR n(CO)NR-2, -NR n(CO)OR 1, -
NRnCOR1, -(S02)NR'2), -NRnSO2R1, -(CH2)õNR12, or optionally substituted aryl,
aralkyl, or C1-C5 alkyl. In the preceding, u is 0 to 5, each R1 and Rn are,
independently,
-H, aryl, or aralkyl, C1-C5 alkyl, or C1-C5 haloalkyl, and each R' is
independently -H,
aryl, aralkyl, or C1-C5 alkyl, or NRm2 is a nonaromatic heterocyclic group.
Even more preferably, R3 in structural Formula I is represented by one of
structural formulas R3-i' to R3-v':
N
(R1 1%, (R11),, (R11),
R3-i' R3-ii' R3-iii'
S
(R11),,
(R11),,
R3-iv' R3-v'
In structural formulas R3-i' to R3-v', w is 0, 1, 2, or 3, and each RI I is
independently -OH, -NO2, -F, -Cl, -Br, C1-C4 alkyl, C1-C4 alkoxy, -CF3, or -
OCF3.
More preferably, R11 is represented by one of structural formulas R11-i to
R11-xxiii:
N N S/\ ",CN\> O
HN-N S S S O
R11-i R11-ii R11-iii R11-iv R11-v R11-vi R11-vii
)JNJCN
N HN HN
F R11-x R11-xi R11-xii R11-xiii
R11-viii R11-ix
AANH ~NH ~NH ,O.N~
NH i i i H
OH ,O NH2 HNC
R11-xvi R11-xviii
R11-xiv R11-xv R11-xvii
O
N,N~L, -(PO)(OR)2 -P(OR)3 -O(PO)(OR)2 -B(OR)2
H R11-xx R11-xxi R11-xxii R11-xxiii
R11-xix
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wherein R is independently -H, aryl, or aralkyl, C1-C5 alkyl, or C1-C5
haloalkyl.
Still more preferably, R3 is represented by one of structural formulas R3a to
R3`.
'-.~~O > 0
OO
OMe
R3a Rib
F I CI I \/
F F 0:F CI I F
OMe
R3C R3" R30 Rat
CI CI
CI CI McMe CI CI
CI OH
R39 R3h RV Rai
F ~ \ \ F
CI a OH OH I OEt Y
OH F
R3h RV Ram R3"
_ S
N
R3 R3P R3q R3r
Most preferably, R3 is represented by structural formula R3e, or R3 is
perfluorinated phenyl or tretrazole.
R4 in structural Formula I is optionally further substituted as described
below
in the section describing suitable substituents for aryl, heteroaryl,
aliphatic, and
cycloalkyl groups. More preferably, R4 is a substituted phenyl, pyridyl,
pyrimidyl,
pyrazyl, naphthyl, biphenyl, phenyl-pyridyl, quinolinyl, benzopyrimidyl,
benzopyrazyl, cyclopropyl, cyclobutyl, cyclopentyl, cyclopentenyl, cyclohexyl,
cyclohexenyl, or a C2-C8 alkenyl group.
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More preferably, R4 is represented by one of structural formulas R4-i to R4-
vii:
(R10)m
X (R10)m P(( (R10)m P(c
(CO)R8 O)R8 O
)R8
R44 (R10)m R4-ii (R10)m R4-vi
(R10)m (RIO). (R10)m
R9 --C C
$ (CO)R8 (R10)m
(CO)R8 D
(CO)R8 (RIO).
(CO)R8
R4-iii R4-iv R4-v R4-vii
In structural formulas R4-i to R4-vii, each m is independently 0, 1, 2, or 3,
and
X is -N-, -CH-, or -CR10-; Ring B is C3-C6 cycloalkyl or C3-C6 cycloalkenyl;
Rings
C and D are each independently aryl or heteroaryl; R8 is -OR q or -NR'2; R9 is
-H,
aryl, aralkyl, or C1-C6 aliphatic; each R10 is independently halogen, -CN, -
NO2, -
CF3, -OCF3, -OR', -(CO)R', -(CO)OR', -O(CO)R', -(CO)O(CO)R', -(CS)R', -
(SO)OR',
-SO3R', -CONR2, -O(CO)NR2, -NRk(CO)NR2, -NR(CO)OR', -NR'COR', -
(SO2)NR2, -NR'SO2R', -(CH2)rNR2, or optionally substituted aryl, aralkyl or C1-
C5
alkyl; the variable t is 0 to 5 and each R' and Rk are, independently, -H,
aryl, aralkyl,
C1-C5 alkyl, or C1-C5 haloalkyl; each R and R' are, independently, -H, aryl,
aralkyl,
or C1-C5 alkyl, or each NR2 and NR'2 are, independently, a nonaromatic
heterocyclic
group; and Rq is -H or optionally substituted aryl, aroyl, aralkyl,
aralkanoyl, C1-C5
alkyl, or C1-C5 alkanoyl.
Even more preferably, R4 is represented by one of structural formulas R4-i' to
R4-vii':
(RIO). 61(CO)R8 (R10)N (R70)m
(CO)R8 \ (CO)R8 (R10)m
R4-i' R4-ii' R4-iii'
(R10)m
(R10)m (R10)m
R9
',~7 "'Q (CO)RS
(CO)R8 (CO)R8 (CO)R8 R4-vii'
R4-iv' R4-v' R4-vi'
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In structural formulas R4-i' to R4-vii', each m is independently 0, 1, 2, or
3; R8
is -OH, C1-C5 alkoxy, or C1-C5 alkanoyloxy; R9 is -H or C1-C6 aliphatic; and
each
R10 is independently -OH, -NO2, -F, -Cl, -Br, C1-C4 alkyl, C1-C4 alkoxy, -CF3,
or -
OCF3.
More preferably, R4 is aryl (e.g. phenyl) which is substituted by one of
structural formulas R10-i to R10-xix:
N~N -1,CN
S O
HN-N S O
R10-i R10-ii R10-iii R10-iv R10-v R10-vi R10-vii
F H N ~i N ~N
NII' ~ HN- HN-P O O~
N
F R10-x R10-xi R10-xii R10-xiii
R10-viii R10-ix
ANH ANH NH NH 6OOH
OH ,O NH2 HNC
R10-xiv R1 0-xv R10-xvi R1 0-xvii R10-xviii
H 0
N,N~
H
R10-xix
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Still more preferably, R4 is represented by one of structural formulas R4a to
R4 q:
\ (CO)R8 I \ (CO)R8 I (CO)R8 (CO)R8
I
CI / / / t -Bu 'C
CI t-Bu
R4=a Rob R4 R4d
i i
(CO)R8 (CO)R8 I (CO)R8e (CO)R8
/ Me" ~%
Me F
R4e R41 Roe R4h
(CO)R8 (CO)R8 (CO)R8 N/ (CO)R8
iN
R4' R41 R4k R4'
(CO)R8
/
(CO)R8 ~(CO)R8 Me
~(CO)RS
Rom R4^ R4 R4p
R41 / -\(CO)R8
Most preferably, R4 is represented by structural formula R4a or R4b, or R4 is
phenyl substituted with tetrazole.
In R4a to R4q, R8 is -NRy2, -OH, C1-C5 alkoxy, or C1-C5 alkanoyloxy,
wherein each Rv is independently -H or C1-C3 alkyl. Even more preferably, R8
is -
OH or C1-C4 alkoxy, or still more preferably, -OH, -OCH3, or -OCH2CH3. Most
preferably, R8 is OCH3 or -OCH2CH3.
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In a preferred embodiment, R5 is:
N,//N 1 ~N ",,C
O
HN-N S S DI S O
N,N J~j CN
N> HN HN-J O
F
NH NH NH ANH H
OH O NH2 HNC
H O
"IN,Nfl"'
H
In a most preferred embodiment, R5 is -H or -CO2H.
In preferred embodiments, in structural Formula I, R8 is -OH, OCH3 or-
OCH2CH3.
In structural Formula I, R3 is represented by one of structural formulas R3-i
to
R3-v or R4 is represented by one of structural formulas R4-i to R4-vii. More
preferably, R3 is represented by one of structural formulas R3-i to R3-v and
R4 is
represented by one of structural formulas R4-i to R4-vii. In still another
embodiment,
in structural Formula I, R3 is represented by one of structural formulas R3-i'
to R3-v'
or R4 is represented by one of structural formulas R4-i' to R4-vii'. More
preferably,
R3 is represented by one of structural formulas R3-i' to R3-v' and R4 is
represented by
one of structural formulas R4-i' to R4-vii'. In another preferred embodiment,
for
structural Formula I, R3 is represented by one of structural formulas R3a to
R3', or R4
is represented by one of structural formulas R4a to R4q. Preferably, R3 is
represented
by one of structural formulas R3a to R3', and R4 is represented by one of
structural
formulas R4a to R4q. More preferably, R3 is represented by structural formula
R3d,
R3e, or R3f, or R4 is represented by structural formula R4a, R4c, or R4e. Even
more
preferably, R3 is represented by structural formula R3d, R3e, or R3f, and R4
is
represented by structural formula R4a, R4c, or R4e.
In another embodiment of Formula I, ring A is a phenyl moiety; J is N(H); R3
is phenyl optionally substituted one or more times with halogen or tetrazole;
L is (CO)
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or (CH2); R4 is phenyl optionally independently substituted one or more times
with
halogen, CO2H, or tetrazole; and R5 is H.
In another embodiment, the compound of formula I is of the formula 5:
R"
A 1R
J N ~
R3
5 wherein J and R3 are the same as previously defined, A is a diazole,
dioxolane,
dioxane or benzene ring and R' and R" are each independently a hydrogen,
halogen,
carboxylic acid, alkyl, heterocycle, nitrile or hydroxyamide.
In yet another embodiment, the compound of formula I is of the formula 6:
A R5 R"
N, R,
Y
R3
6
wherein J, R3 and R5 are the same as previously defined, Y is C=O or CH2, A
is a diazole, dioxolane, dioxane or benzene ring and R' and R" are each
independently a hydrogen, halogen, carboxylic acid, alkyl, heterocycle,
nitrile or
hydroxyamide.
In another embodiment, the compound is of formula I, wherein ring A is an
aryl moiety; J is N(H); R3 is aryl optionally substituted one or more times
with
halogen or a heteroaryl; L is (CO) or (CH2); R4 is phenyl optionally
independently
substituted one or more times with halogen, CO2H, or a heteroaryl; R5 is H,
alkyl,
alkoxyl, CO2H or CO2alkyl; and R6 is H, alkyl or alkoxyl.
In yet another embodiment, the compound is of formula I, wherein ring A is a
phenyl moiety; J is N(H); R3 is phenyl optionally substituted one or more
times with
halogen or tetrazole; L is (CO) or (CH2); R4 is phenyl optionally
independently
substituted one or more times with halogen, CO2H, or a heteroaryl; R5 is H or
CO2H;
and R6 is H.
In another embodiment, the compound is of formula I, wherein ring A is a
phenyl moiety; J is N(H); R3 is phenyl optionally substituted with tetrazole;
L is CH2;
and R4 is phenyl optionally independently substituted one or more times with
halogen.
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In other embodiments the compound, the compound of the method, and the
compound of the pharmaceutical composition are each represented by the
individual
compounds provided in Table 1:
Table 1
Compound # Structure
1 /
N
O O
HO
N
O~H
2 CI
'Cl
\ O O
H
O
3
O O
4H~
4
~-OH
O
N HO O
/ \
':~'H N
N
N -rl
/ HO O
00
H / \
N
6 CI CI
I \ \ N O
O HO
N
H
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7
N~
\ I" F
"
N
N
H
N
8
(:~'H %NX
9
N J
ON
H
O
N
N O
H
HO
1 1 H L CI
\ c / CI
N-
N
H
O
N HO O
\ /
1 HO CI
O / CI
/ \ I
DN
N
H
H O
\ /
13 Cl
CI
N
H
O
N HO O
\ /
13
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14 /
,moo
N
- CI
N
H
CI
15 /
O
~ \ N \ I
N
H
16
0
CI
O
/ \ CI
Q 1 N
C
N
H
O
/ IN HO
O
HN
17 CI
Cl
0
0
' N H-
O NI OH
18 \
0
O
N~ HO O
19
0
O 0 OH
Z"I'
O
\ N
()--~ OH
N
H
\ / N
14
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21
N
H
\ / N
22
N
H
\ / N
23
N CI
H
\ / N
24 0
O
N
N OH
H
O
N
25 CI CI
N O
O / \ O HO
N /
O
26 CON
O
N 0 OH
27 / CI
O CI
N
H O SOH
/ 0 H
N \
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28 -~
0
N
N
29 0
>==
I ~ \ N
N \ %\II
H
N
N
/N H
30 / \
::' N N,
NH
CI
31 HOB
N / N
N N-NH
H O
CI \
CI
32 Qo
HN N
CI
N
HN
CI
33
0
QN(O/N
N-NH
H O
CI
CI
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34 =O
N
N
N N-NH
H O
CI
CI
35 -0
>==o
\ N-N
~~ N I \ /N\~
N H
H
F
36
O
\ N
N I \ N
N /
F
F"Q- 37 '0
0
N N / ~
H
O N
HN N
O
38 HO
O
N
H
\ O N
N
HNC
O N 11//
39
OH
9H N
N
\ \ /
F \
F HN_ //N
N
17
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40 HO
0
\ NON
~H
F
41 /
N
N
H yl:~y \N
CI O N~ NH
CI
42 QoN y N
\ 0 N- H
N
N-NH
43 /
N
yl:~Y \N N
O N- H
O
44 /
N
N
H
N
O ~ \\N
HO
0
45 H \\ N
NN N
F
/ \ \
HN N
OH
0
18
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46 H -\\
NN N
F
/
HN N
N NH
N
47
F
qHN
N N \
\
N
\ N-NH
I
O
48 / \ N- NON
H
HN N
CI
\
CI /
49 /
\ O
HN N Q N \
\ N
CI N~NH
CI /
/
50 HO
O
HN N I N \
N
CI N-NH
CI
51 CI
/ \ \ CI
N N
H
O
O OH
N
I
N\\ N F
19
CA 02707442 2010-05-28
WO 2009/102377 PCT/US2008/084832
52 /
N ~
/
/ O OH
N\\ N F
53
\ CI
H N / CI
N
H
N
F N`
54
N
H
N
I ~ H
N
F N- e
55 /
F
H N
N
N\
H
/
F N,
56 N
N
H
I ~ H
N
F N- e
57 HO
HN )CN N
N
CI = N-NH
CI /
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58 0/ cl
C CI
O SOH
/ O H
N \
59 CI
\ CI
N I N
H
CI O
/ I OH
H
CI
HN N
\N
N,N/
H
61
HN CI
CI
\N
N N/
H
62
CI
HN N
\N
N N
H
21
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WO 2009/102377 PCT/US2008/084832
63
HN N
\ N
N- NH
64 /
HN N
N
\ N- NH
O / O
HN N
F
F
I N
N N
H
66 H2N
O
HN N N
N
CI = N-NH
CI /
22
CA 02707442 2010-05-28
WO 2009/102377 PCT/US2008/084832
67 cl
N
HN cl
N
N~ NI
H
68
\ c\
HN N
NN
N~
H
69
N O
HN
N
III
N
NN
H
70 0
HN N
\N
N N
H
23
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71 HO
O
'N
O
O HO
%F,5~
72 HO
qG / \
HN
F O
HO O
F
73 ol-~
HN N
%N
N N/
H
74
HN N
\N
N
H
24
CA 02707442 2010-05-28
WO 2009/102377 PCT/US2008/084832
HN N
%N
N N
H
76
HN N
\N
N~ N
H
77
F
HN N
N
N- N/
H
78
HN N /
\N
N,N
H
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79 -
HN N
CI
CI
NH
N
H
HO O
81
NH
N
H
O O
82
N CI
N
H
CI
N
26
CA 02707442 2010-05-28
WO 2009/102377 PCT/US2008/084832
83
/ I OH
H
H
O
N
84
H
INI
HN
= N
F :C
/
O
86 9H -O
eN
N
CI =
CI
27
CA 02707442 2010-05-28
WO 2009/102377 PCT/US2008/084832
87
F
I I \
HN N
N
O O
88
F
H N
N
N
89 YO
HN N
I \ N
CI - N~ NH
CI
O
NH
N
H
F
F
28
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91 o
0
NH
N
H
F -
F /
92
N
HN
CI
CI
NH
NON
93 / HO
I ' 0
HN N
qN
N
:iiiiiiicii N-NH
/
94
_ I \
HN N N
\
N-NH
29
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WO 2009/102377 PCT/US2008/084832
I N H
N
H
NON
F
F
96
HN I N \N
I-NH
CI
97
0
~INH
N
H
\ N
98
HN N N
N
N- NH
CI CI
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99 /
_ I N I ~ N
HN
N
N-NH
F / F
100
HN N N
\N
N- NH
101
HN N \N
I-NH
102
HN N
N
N- NH
_0~ 0
31
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103
qH jN
F
HO O
104
HN KN
N
N-NH
105 /
HN N
N
\ N- NH
O /
106 /
O
HN N
F O
HO 0
F
32
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107
I
HN N
N
N_NH
In a particular embodiment, the compounds of Table 1 can be used to treat a
bacterial infection in a subject in need thereof.
In another embodiment, compounds 4, 13, 22, 32, 49, 67, 71 and 72 can be
used to treat a bacterial infection in a subject in need thereof.
As used herein, a "subject" includes mammals, e.g., humans, companion
animals (e.g., dogs, cats, birds, aquarium fish, reptiles, and the like), farm
animals
(e.g., cows, sheep, pigs, horses, fowl, farm-raised fish and the like) and
laboratory
animals (e.g., rats, mice, guinea pigs, birds, aquarium fish, reptiles, and
the like).
Alternatively, the subject is a warm-blooded animal. More preferably, the
subject is a
mammal. Most preferably, the subject is human.
A subject in need of treatment has a bacterial infection (or has been exposed
to
an infectious environment where bacteria are present, e.g., in a hospital) the
symptoms of which may be alleviated by administering an effective amount of
the
disclosed bicyclic derivatives. For example, a subject in need of treatment
can have
an infection for which the disclosed bicyclic derivatives can be administered
as a
treatment. In another example, a subject in need of treatment can have an open
wound or burn injury, or can have a compromised immune system, for which the
disclosed PPAT inhibitors can be administered as a prophylactic. Thus, a
subject can
be treated therapeutically or prophylactically. More preferably, a subject is
treated
therapeutically.
Typically, the subject is treated for a bacterial infection caused by a
bacteria of
a genus selected from Allochromatium, Acinetobacter, Bacillus, Campylobacter,
Chlamydia, Chlamydophila, Clostridium, Citrobacter, Escherichia, Enterobacter,
Enterococcus, Francisella, Haemophilus, Helicobacter, Klebsiella, Listeria,
Moraxella, Mycobacterium, Neisseria, Proteus, Pseudomonas, Salmonella,
erratia,
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WO 2009/102377 PCT/US2008/084832
Shigella, Stenotrophomonas, Staphyloccocus, Streptococcus, Synechococcus,
Vibrio,
and Yersina.
More preferably, the subject is treated for a bacterial infection from
Allochromatium vinosum, Acinetobacter baumanii, Bacillus anthraces,
Campylobacterjejuni, Chlamydia trachomatis, Chlamydia pneumoniae, Clostridium
spp., Citrobacter spp., Escherichia coli, Enterobacter spp.,
Enterococcusfaecalis.,
Enterococcus faecium, Francisella tularensis, Haemophilus influenzas,
Helicobacterpylori, Klebsiella spp., Listeria moiwcytogenes, Moraxella
catarrhalis,
Mycobacterium tuberculosis, Neisseria meningitides, Neisseria gonorrhoeae,
Proteus
mirabilis, Proteus vulgaris, Pseudomonas aeruginosa, Salmonella spp., Serratia
spp.,
Shigella spp., Stenotrophomonas maltophilia, Staphyloccocus aureus,
Staphyloccocus
epidermidis, Streptococcus pneumoniae, Streptococcus pyogenes, Streptococcus
agalactiae, Yersinapestis, and Yersina enterocolitica, and the like.
Preferably, the subject is treated for a bacterial infection caused by a
bacterium that expresses a PPAT protein. As used herein, a PPAT protein is a
phosphopantetheine adenytransferase enzyme, i.e., systematic name
ATP:pantetheine-
4'-phosphate adenylyltransferase, IUBMB systematic classification EC 2.7.7.3,
(see
International Union of Biochemistry and Molecular Biology,
www.chem.qmul.ac.uk/iubmb/).
In one embodiment, a subject is also concurrently treated for a fungal
infection, for example, a fungal infection caused by a pathogenic
dermatophyte, e.g., a
species of the genera Trichophyton, Tinea, Microspormn, Epidermophyton and the
like; or a pathogenic filamentous fungus, e.g., a species of genera such as
Aspergillus,
Histoplasma, Cryptococcus, Microspormn, and the like; or a pathogenic non-
filamentous fungus, e.g., a yeast, for example, a species of the genera
Candida,
Malassezia, Trichosporon, Rhodotorula, Torulopsis, Blastomyces,
Paracoccidioides,
Coccidioides, and the like. Preferably, the subject is concurrently treated
for a fungal
infection resulting from a species of the genera Aspergillus or Trichophyton.
Species
of Trichophyton include, for example, T. mentagrophytes, T. rubrum, T.
schoenleinii,
T. tonsurans, T. verrucosum, and T. violaceum. Species of Aspergillus include,
for
example, A. fumigatus, A.flavus, A. niger, A. amstelodami, A. candidus, A.
carneus, A.
nidulans, A oryzae, A. restrictus, A. sydowi, A. terreus, A. ustus, A.
versicolor, A.
caesiellus, A. clavatus, A. avenaceus, and A. deflectus. More preferably, the
subject is
concurrently treated therapeutically for a fungal infection caused by a
species of the
34
CA 02707442 2010-05-28
WO 2009/102377 PCT/US2008/084832
genus Aspergillus selected from A. fumigatus, A. flavits, A. niger, A.
canstelodami, A.
candidus, A. carneus, A. nidulans, A oryzae, A. restrictus, A. sydowi, A.
terreus, A.
ustus, A. versicolor, A. caesiellus, A. clavatus, A. avenaceus, and. A.
deflectus. Even
more preferably the subject is concurrently treated therapeutically for a
fungal
infection caused by Aspergillus fumigatus or A spergillus niger, and most
preferably,
Aspergillus fumigatus.
An "effective amount" of a compound of the disclosed invention is the
quantity that, when administered to a subject in need of treatment, improves
the
prognosis of the subject, e.g., delays the onset of and/or reduces the
severity of one or
more of the subject's symptoms associated with a bacterial infection. The
amount of
the disclosed compound to be administered to a subject will depend on the
particular
disease, the mode of administration, co-administered compounds, if any, and
the
characteristics of the subject, such as general health, other diseases, age,
sex,
genotype, body weight and tolerance to drugs. The skilled artisan will be able
to
determine appropriate dosages depending on these and other factors. Effective
amounts of the disclosed compounds typically range between about 0.01 mg/kg
per
day and about 100 mg/kg per day, and preferably between 0.1 mg/kg per day and
about 10 mg/kg/day. Techniques for administration of the disclosed compounds
of
the invention can be found in Remington: the Science and Practice of Pharmacy,
l91h
edition, Mack Publishing Co., Easton, PA (1995), the entire teachings of which
are
incorporated herein by reference.
A "pharmaceutically acceptable salt" of the disclosed compound is a product
of the disclosed compound that contains an ionic bond, and is typically
produced by
reacting the disclosed compound with either an acid or a base, suitable for
administering to a subject.
For example, an acid salt of a compound containing an amine or other basic
group can be obtained by reacting the compound with a suitable organic or
inorganic
acid, such as hydrogen chloride, hydrogen bromide, acetic acid, perchloric
acid and
the like. Compounds with a quaternary ammonium group also contain a
counteranion
such as chloride, bromide, iodide, acetate, perchlorate and the like. Other
examples of
such salts include hydrochlorides, hydrobromides, sulfates, methanesulfonates,
nitrates, maleates, acetates, citrates, fumarates, tartrates (e.g. (+)-
tartrates, (-)-tartrates
or mixtures thereof including racemic mixtures), succinates, benzoates and
salts with
amino acids such as glutamic acid.
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Salts of compounds containing a carboxylic acid or other acidic functional
groups can be prepared by reacting with a suitable base. Such a
pharmaceutically
acceptable salt may be made with a base which affords a pharmaceutically
acceptable
cation, which includes alkali metal salts (especially sodium and potassium),
alkaline
earth metal salts (especially calcium and magnesium), aluminum salts and
ammonium
salts, as well as salts made from physiologically acceptable organic bases
such as
trimethylamine, triethylamine, morpholine, pyridine, piperidine, picoline,
dicyclohexylamine, N, N'-dibenzylethylenediamine, 2-hydroxyethylamine, bis-(2-
hydroxyethyl)amine, tri-(2-hydroxyethyl)amine, procaine, dibenzylpiperidine, N-
benzyl-3-phenethylamine, dehydroabietylamine, N,N'-bisdehydroabietylamine,
glucamine, N-methylglucamine, collidine, quinine, quinoline, and basic amino
acid
such as lysine and arginine.
Certain compounds and their salts may also exist in the form of solvates, for
example hydrates, and the present invention includes each solvate and mixtures
thereof.
As used herein, a "pharmaceutical composition" is a formulation containing
the disclosed compounds in a form suitable for administration to a subject.
The
pharmaceutical composition can be in bulk or in unit dosage form. The unit
dosage
form can be in any of a variety of forms, including, for example, a capsule,
an IV bag,
a tablet, a single pump on an aerosol inhaler, or a vial. The quantity of
active
ingredient (i.e., a formulation of the disclosed compound or salts thereof) in
a unit
dose of composition is an effective amount and may be varied according to the
particular treatment involved. It is appreciated that it may be necessary to
make
routine variations to the dosage depending on the age and condition of the
patient.
The dosage will also depend on the route of administration. A variety of
routes are
contemplated, including topical, oral, pulmonary, rectal, vaginal,
parenternal,
transdermal, subcutaneous, intravenous, intramuscular, intraperitoneal and
intranasal.
The compounds described herein, and the pharmaceutically acceptable salts
thereof, can be used in pharmaceutical preparations in combination with a
pharmaceutically acceptable carrier or diluent. Suitable pharmaceutically
acceptable
carriers include inert solid fillers or diluents and sterile aqueous or
organic solutions.
The compounds will be present in such pharmaceutical compositions in amounts
sufficient to provide the desired dosage amount in the range described herein.
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Techniques for formulation and administration of the disclosed compounds of
the
Invention can be found in Remington: the Science and Practice of Pharmacy,
above.
For oral administration, the disclosed compounds or salts thereof can be
combined with a suitable solid or liquid carrier or diluent to form capsules,
tablets,
pills, powders, syrups, solutions, suspensions and the like.
The tablets, pills, capsules, and the like contain from about 1 to about 99
weight percent of the active ingredient and a binder such as gum tragacanth,
acacias,
corn starch or gelatin; excipients such as dicalcium phosphate; a
disintegrating agent
such as corn starch, potato starch or alginic acid; a lubricant such as
magnesium
stearate; and/or a sweetening agent such as sucrose, lactose or saccharin.
When a
dosage unit form is a capsule, it may contain, in addition to materials of the
above
type, a liquid carrier such as a fatty oil.
Various other materials may be present as coatings or to modify the physical
form of the dosage unit. For instance, tablets may be coated with shellac,
sugar or
both. A syrup or elixir may contain, in addition to the active ingredient,
sucrose as a
sweetening agent, methyl and propylparabens as preservatives, a dye and a
flavoring
such as cherry or orange flavor, and the like.
For parental administration of the disclosed compounds, or salts, solvates, or
hydrates thereof, can be combined with sterile aqueous or organic media to
form
injectable solutions or suspensions. For example, solutions in sesame or
peanut oil,
aqueous propylene glycol and the like can be used, as well as aqueous
solutions of
water-soluble pharmaceutically-acceptable salts of the compounds. Dispersions
can
also be prepared in glycerol, liquid polyethylene glycols and mixtures thereof
in oils.
Under ordinary conditions of storage and use, these preparations contain a
preservative to prevent the growth of microorganisms.
In addition to the formulations previously described, the compounds may also
be formulated as a depot preparation. Suitable formulations of this type
include
biocompatible and biodegradable polymeric hydrogel formulations using
crosslinked
or water insoluble polysaccharide formulations, polymerizable polyethylene
oxide
formulations, impregnated membranes, and the like. Such long acting
formulations
may be administered by implantation or transcutaneous delivery (for example
subcutaneously or intramuscularly), intramuscular injection or a transdermal
patch.
Preferably, they are implanted in, or applied to, the microenvironment of an
affected
organ or tissue, for example, a membrane impregnated with the disclosed
compound
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WO 2009/102377 PCT/US2008/084832
can be applied to an open wound or burn injury. Thus, for example, the
compounds
may be formulated with suitable polymeric or hydrophobic materials, for
example, as
an emulsion in acceptable oil, or ion exchange resins, or as sparingly soluble
derivatives, for example, as a sparingly soluble salt.
For topical administration, suitable formulations may include biocompatible
oil, wax, gel, powder, polymer, or other liquid or solid carriers. Such
formulations
may be administered by applying directly to affected tissues, for example, a
liquid
formulation to treat infection of conjunctival tissue can be administered
dropwise to
the subject's eye, a cream formulation can be administer to a wound site, or a
bandage
may be impregnated with a formulation, and the like.
For rectal administration, suitable pharmaceutical compositions are, for
example, topical preparations, suppositories or enemas.
For vaginal administration, suitable pharmaceutical compositions are, for
example, topical preparations, pessaries, tampons, creams, gels, pastes, foams
or
sprays.
In addition, the compounds may also be formulated to deliver the active agent
by pulmonary administration, e.g., administration of an aerosol formulation
containing the active agent from, for example, a manual pump spray, nebulizer
or
pressurized metered-dose inhaler. Suitable formulations of this type can also
include
other agents, such as antistatic agents, to maintain the disclosed compounds
as
effective aerosols.
The term "pulmonary" as used herein refers to any part, tissue or organ whose
primary function is gas exchange with the external environment, i.e., 02/CO2
exchange, within a patient. "Pulmonary" typically refers to the tissues of the
respiratory tract. Thus, the phrase "pulmonary administration" refers to
administering
the formulations described herein to any part, tissue or organ whose primary
function
is gas exchange with the external environment (e.g., mouth, nose, pharynx,
oropharynx, laryngopharynx, larynx, trachea, carina, bronchi, bronchioles,
alveoli).
For purposes of the present invention, "pulmonary" is also meant to include a
tissue
or cavity that is contingent to the respiratory tract, in particular, the
sinuses.
A drug delivery device for delivering aerosols comprises a suitable aerosol
canister with a metering valve containing a pharmaceutical aerosol formulation
as
described and an actuator housing adapted to hold the canister and allow for
drug
delivery. The canister in the drug delivery device has a head space
representing
38
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WO 2009/102377 PCT/US2008/084832
greater than about 15% of the total volume of the canister. Often, the polymer
intended for pulmonary administration is dissolved, suspended or emulsified in
a
mixture of a solvent, surfactant and propellant. The mixture is maintained
under
pressure in a canister that has been sealed with a metering valve.
For nasal administration, either a solid or a liquid carrier can be used. The
solid carrier includes a coarse powder having particle size in the range of,
for
example, from about 20 to about 500 microns and such formulation is
administered by
rapid inhalation through the nasal passages. Where the liquid carrier is used,
the
formulation may be administered as a nasal spray or drops and may include oil
or
aqueous solutions of the active ingredients.
In addition to the formulations described above, a formulation can optionally
include, or be co-administered with one or more additional drugs, e.g., other
antibiotics, anti-inflammatories, antirungals, antivirals, immunomodulators,
antiprotozoals, steroids, decongestants, bronchodialators, and the like. For
example,
the disclosed compound can be co-administered with drugs such as such as
ibuprofen,
prednisone (corticosteroid) pentoxifylline, Amphotericin B, Fluconazole,
Ketoconazol, Itraconazol, penicillin, ampicillin, amoxicillin, and the like.
The
formulation may also contain preserving agents, solubilizing agents, chemical
buffers,
surfactants, emulsifiers, colorants, odorants and sweeteners.
The term "derivative," e.g., in the term "bicyclic derivatives," refers to
compounds that have a common core structure, and are substituted with various
groups as described herein. For example, all of the compounds represented by
structural Formula I are tetrahydro-(3-carboline derivatives, and have
structural
Formula I as a common core.
In the structural formulas depicted herein, a dashed line indicates a bond by
which the depicted or moiety or group is connected to the remainder of the
molecule.
For example, the dashed line in R4-i indicates the bond that connects the
depicted
group to another structural formula. A dashed or solid line across a bond in a
ring, for
example, the solid line from R11 in R4-i, indicates that the represented bond
can be
connected to any substitutable atom in the ring. A zig-zag line indicates
either cis or
trans arrangement of the respective substituents with respect to the bond
represented
by the dashed line.
The term "aryl" group refers to carbocyclic aromatic groups such as phenyl,
naphthyl, and anthracyl. The term "heteroaryl" group refers to heteroaromatic
groups
39
CA 02707442 2010-05-28
WO 2009/102377 PCT/US2008/084832
such as imidazolyl, isoimidazolyl, thienyl, furanyl, pyridyl, pyrimidyl,
pyranyl,
pyrazolyl, pyrrolyl, pyrazinyl, thiazolyl, isothiazolyl, oxazolyl,
isooxazolyl, 1,2,3-
triazolyl, 1,2,4-triazolyl, and tetrazolyl. As used herein, a "heteroaryl"
group is a 5
membered carbocyclic ring containing at least one N, S, or 0 atom and two
double
bonds, or a 6 membered carbocyclic ring containing at least one N, S, or 0
atom and
three double bonds.
The term "nonaromatic heterocyclic" refers to non-aromatic ring systems
typically having four to eight members, preferably five to six, in which one
or more
ring carbons, preferably one to four, are each replaced by a heteroatom such
as N, 0,
or S. Examples of non-aromatic heterocyclic rings include 3-tetrahydrofuranyl,
2-
tetrahydropyranyl, 3-tetrahydropyranyl, 4-tetrahydropyranyl, [1,3]-dioxalanyl,
[1,3]-
dithiolanyl, [1,3]-dioxanyl, 2-tetrahydrothiophenyl, 3-tetrahydrothiophenyl, 2-
morpholinyl, 3-morpholinyl, 4-raorpholinyl, 2-thiomorpholinyl, 3-
thiomorpholinyl, 4-
thiomorpholinyl, 1-pyrrolidinyl, 2-pyrrolidinyl, 3-pyrorolidinyl, 1-
piperazinyl, 2-
piperazinyl, 1-piperidinyl, 2-piperidinyl, 3-piperidinyl, 4-piperidinyl, 4-
thiazolidinyl,
5-diazolonyl, N-substituted diazolonyl, and 1-pthalimidinyl.
The disclosed compounds can contain one or more chiral centers. The
presence of chiral centers in a molecule gives rise to stereoisomers. For
example, a
pair of optical isomers, referred to as "enantiomers", exist for every chiral
center in a
molecule. A pair of diastereomers exists for every chiral center in a compound
having two or more chiral centers. Where the structural formulas do not
explicitly
depict stereochemistry, for example in structural Formula I, it is to be
understood that
these formulas encompass enantiomers free from the corresponding optical
isomer,
racemic mixtures, mixtures enriched in one enantiomer relative to its
corresponding
optical isomer, a diastereomer free of other diastereomers, a pair of
diastereomers free
from other diasteromeric pairs, mixtures of diasteromers, mixtures of
diasteromeric
pairs, mixtures of diasteromers in which one diastereomer is enriched relative
to the
other diastereomer(s) and mixtures of diasteromeric pairs in which one
diastereomeric
pair is enriched relative to the other diastereomeric pair(s).
The term "alkyl" used alone or as part of a larger moiety (e.g., aralkyl,
alkoxy,
alkylamino, alkylaminocarbonyl, haloalkyl), is a straight or branched non-
aromatic
hydrocarbon which is completely saturated. Typically, a straight or branched
alkyl
group has from 1 to about 10 carbon atoms, preferably from 1 to about 5 if not
otherwise specified. Examples of suitable straight or branched alkyl groups
include
CA 02707442 2010-05-28
WO 2009/102377 PCT/US2008/084832
methyl, ethyl, n-propyl, 2-propyl, w-butyl, sec-butyl, tert-butyl, pentyl,
hexyl, heptyl
or octyl. A C1-C10 straight or branched alkyl group or a C3-C8 cyclic alkyl
group
can also be referred to as a "lower alkyl" group. An "alkoxy" group refers to
an alkyl
group that is connected through an intervening oxygen atom, e.g., methoxy,
ethoxy, 2-
propyloxy, tert-butoxy, 2-butyloxy, 3-pentyloxy, and the like.
The terms "optionally halogenated alkyl" and "optionally halogenated
alkoxy", as used herein, includes the respective group substituted with one or
more of
-F, -Cl, -Br, or-I.
The terms "alkanoyl," "aroyl," and the like, as used herein, indicates the
respective group connected through an intervening carbonyl, for example, -
(CO)CH2CH3, benzoyl, and the like. The terms "alkanoyloxy", "aroyloxy", and
the
like, as used herein, indicates the respective group connected through an
intervening
carboxylate, for example, -O(CO)CH2CH3, -O(CO)C6H5, and the like.
The term "cycloalkyl group" is a cyclic alkyl group has from 3 to about 10
carbon atoms, preferably from 3 to about 7. Examples of suitable cycloalkyl
groups
include cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, cycloheptyl and
cyclooctyl.
A "cycloalkoxy" group refers to a cycloalkyl group that is connected through
an
intervening oxygen atom, e.g., cyclopentyloxy, cyclohexyloxy, and the like.
The term "aliphatic" includes branched and linear alkyl groups that contain
one or more units of carbon-carbon unsaturation, i.e., carbon-carbon double or
triple
bonds. A cycloaliphatic group is a cyclic aliphatic group, for example,
cyclohexenyl
or cyclopentenyl.
The terms "aralkyl," "heteroaralkyl," "cycloalkylalkyl,"
"cycloaliphaticalkyl,"
and "nonaromatic heterocycloalkyl" refer to aryl, heteroaryl, cycloalkyl,
cycloaliphatic, and nonaromatic heterocyclic groups, respectively, that are
connected
through an alkyl chain, e.g., benzyl, -CH2-CH2- pyridine, (3-
cyclohexyl)propyl, and
the like.
The terms biaryl, biheteroaryl, aryl-heteroaryl and heteroaryl-aryl, as used
herein, indicate two aryl groups connected by a single covalent bond, two
heteroaryl
groups connected by a single covalent bond, an aryl and heteroaryl group
connected
by single covalent bond, and a heteroaryl and aryl group connected by a single
covalent bond, respectively. Examples of biaryl, biheteroaryl, heteroaryl-aryl
and
aryl-heteroaryl groups include biphenyl, bipyridyl, pyrimidyl-phenyl, and
phenyl-
pyridyl, respectively. When a biaryl, biheteroaryl, heteroaryl-aryl or aryl-
heteroaryl
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WO 2009/102377 PCT/US2008/084832
group is a substituent, as in the definition of R4 for structural Formula I,
the first
recited group is bonded to the remainder of the molecule, i.e., "L" in
structural
Formula I. For example, when R4 in structural Formula I is a phenyl-pyridyl
group,
the phenyl of the phenyl-pyridyl group is bonded to L.
An "acyclic" group is a substituent that does not contain a ring. A
"monocyclic" group contains only a single ring, for example, a phenyl ring
that is not
fused to another ring. A "polycyclic" group is a group that contains multiple
fused
rings, for example, naphthyl.
A "substitutable atom" is any atom such as nitrogen or carbon that is bonded
through a single covalent bond to a hydrogen atom, wherein the hydrogen atom
can
be replaced with another group. A "substitutable ring atom" in an aromatic
ring is
any ring atom, e.g., a carbon or nitrogen, which is bonded by a single
covalent bond
to a hydrogen atom, wherein the hydrogen atom can be replaced with another
group.
Suitable substituents are those that do not substantially interfere with the
pharmaceutical activity of the disclosed compound. A compound or group can
have
one or more substituents, which can be identical or different. Examples of
suitable
substituents for a substitutable carbon atom in an alkyl, aliphatic,
cycloalkyl,
cycloaliphatic, non-aromatic heterocyclic, aryl, or heteroaryl group include -
OH,
halogen (-Br, -Cl, -I and -F), -R, -OR, -CH2R, - CH2CH2R, -OCH2R, -CH2OR, -
CH2CH2OR, -CH2OC(O)R, -O-COR, -COR, -SR, -SCH2R, - CH2SR, -SOR, -S02R, -
CN, -NO2, -COOH, -S03H, -NH2, -NHR, -N(R)2, -000R, -CH2COOR, -
CH2CH2COOR, -CHO, -CONH2, -CONHR, -CON(R)2, -NHCOR, -NRCOR, -
NHCONH2, -NHCONRH, -NHCON(R)2, -NRCONH2, -NRCONRH, -NRCON(R)2, -
C(=NH)-NH2, -C(=NH)-NHR, -C(=NH)-N(R)2, -C(=NR)-NH2, -C(=NR)-NHR, -
C(=NR)-N(R)2, -NH-C(=NH)-NH2, -NH-C(=NH)-NHR, -NH-C(=NH)-N(R)2, -NH-
C(=NR)-NH2, -NH-C(=NR)-NHR, -NH-C(=NR)-N(R)2, -NRH-C(=NH)-NH2, -NR-
C(=NH)-NHR, -NR-C(=NH)-N(R)2, -NR-C(=NR)-NH2, -NR-C(=NR)-NHR, -NR-
C(=NR)-N(R)2, -S02NH2, -SO2NHR, -S02NR2, -SH, -SOkR (k is 0,1 or 2) and -NH-
C(=NH)-NH2. Each R is independently an alkyl, cycloalkyl, benzyl, aromatic,
heteroaromatic, or N-anilinyl group that is optionally substituted.
Preferably, R is
unsubstituted. In addition, -N(R)2, taken together, can also form a
substituted or
unsubstituted heterocyclic group, such as pyrrolidinyl, piperidinyl,
morpholinyl and
thiomorpholinyl. Examples of substituents on group represented by R include
amino,
alkylamino, dialkylamino, aminocarbonyl, halogen, alkyl, alkylaminocarbonyl,
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dialkylaminocarbonyloxy, alkoxy, nitro, cyano, carboxy, alkoxycarbonyl,
alkylcarbonyl, hydroxy, haloalkoxy, or haloalkyl.
Suitable substituents on the nitrogen of a heterocyclic group or
heteroaromatic
group include -R', -N(R')2, -C(O)R', -CO2 R, -C(O)C(O)R', -C(O)CH2 C(O)R', -
S02R', -SO2 N(R')2, -C(=S)N(R')2, -C(=NH)-N(R')2, and -NR'S02R', wherein R' is
hydrogen, an alkyl, alkoxy, cycloalkyl, cycloalkoxy, phenyl, phenoxy, benzyl,
benzyloxy, heteroaromatic, or heterocyclic group that is optionally
substituted.
Examples of substituents on the groups represented by R' include amino,
alkylamino,
dialkylamino, aminocarbonyl, halogen, alkyl, alkylaminocarbonyl,
dialkylaminocarbonyloxy, alkoxy, nitro, cyano, carboxy, alkoxycarbonyl,
alkylcarbonyl, hydroxy, haloalkoxy, or haloalkyl. Preferably, R' is
unsubstituted.
Advantageously, the present invention also provides kits for use by a
consumer for treating disease. The kits comprise a) a pharmaceutical
composition
comprising an antibiotic and a pharmaceutically acceptable carrier, vehicle or
diluent;
and, optionally, b) instructions describing a method of using the
pharmaceutical
composition for treating the specific disease. The instructions may also
indicate that
the kit is for treating disease while substantially reducing the concomitant
liability of
adverse effects associated with antibiotic administration.
A "kit" as used in the instant application includes a container for containing
the separate unit dosage forms such as a divided bottle or a divided foil
packet. The
container can be in any conventional shape or form as known in the art which
is made
of a pharmaceutically acceptable material, for example a paper or cardboard
box, a
glass or plastic bottle or jar, a re-sealable bag (for example, to hold a
"refill" of tablets
for placement into a different container), or a blister pack with individual
doses for
pressing out of the pack according to a therapeutic schedule. The container
employed
can depend on the exact dosage form involved, for example a conventional
cardboard
box would not generally be used to hold a liquid suspension. It is feasible
that more
than one container can be used together in a single package to market a single
dosage
form. For example, tablets may be contained in a bottle which is in turn
contained
within a box.
An example of such a kit is a so-called blister pack. Blister packs are well
known in the packaging industry and are being widely used for the packaging of
pharmaceutical unit dosage forms (tablets, capsules, and the like). Blister
packs
generally consist of a sheet of relatively stiff material covered with a foil
of a
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preferably transparent plastic material. During the packaging process,
recesses are
formed in the plastic foil. The recesses have the size and shape of individual
tablets
or capsules to be packed or may have the size and shape to accommodate
multiple
tablets and/or capsules to be packed. Next, the tablets or capsules are placed
in the
recesses accordingly and the sheet of relatively stiff material is sealed
against the
plastic foil at the face of the foil which is opposite from the direction in
which the
recesses were formed. As a result, the tablets or capsules are individually
sealed or
collectively sealed, as desired, in the recesses between the plastic foil and
the sheet.
Preferably the strength of the sheet is such that the tablets or capsules can
be removed
from the blister pack by manually applying pressure on the recesses whereby an
opening is formed in the sheet at the place of the recess. The tablet or
capsule can
then be removed via said opening.
It may be desirable to provide a written memory aid, where the written
memory aid is of the type containing information and/or instructions for the
physician, pharmacist or subject, e.g., in the form of numbers next to the
tablets or
capsules whereby the numbers correspond with the days of the regimen which the
tablets or capsules so specified should be ingested or a card which contains
the same
type of information. Another example of such a memory aid is a calendar
printed on
the card e.g., as follows "First Week, Monday, Tuesday," ... etc.... "Second
Week,
Monday, Tuesday, ... " etc. Other variations of memory aids will be readily
apparent. A "daily dose" can be a single tablet or capsule or several tablets
or
capsules to be taken on a given day.
Another specific embodiment of a kit is a dispenser designed to dispense the
daily doses one at a time. Preferably, the dispenser is equipped with a memory-
aid, so
as to further facilitate compliance with the regimen. An example of such a
memory-
aid is a mechanical counter, which indicates the number of daily doses that,
has been
dispensed. Another example of such a memory-aid is a battery-powered micro-
chip
memory coupled with a liquid crystal readout, or audible reminder signal
which, for
example, reads out the date that the last daily dose has been taken and/or
reminds one
when the next dose is to be taken.
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EXEMPLIFICATION
Example 1: Synthesis of PPAT inhibitors of structural Formula I:
H O
O
A + II J NH +
J I NH2 H R3 ~\ \
1 ? 3 R' R"
4
R"
A R
J
R3 5
R' and R" are, e.g. each indepently a hydrogen, carboxylic acid, halogen,
alkyl, heterocycle, nitrile or hydroxyamide; R3 is, e.g. an optionally
substituted aryl.
To a stirred solution of amine 1 in CH2C12 is added aldehyde 2 followed by
TFA. The resulting solution is heated at reflux overnight. After
concentration, a
formed solid is filtered, washed with hexane, and dried to give 3. 3 is
stirred at
ambient temperature in a vial with DMF, benzaldehdye 4, and AcOH followed by
addition of NaBH(OAc)3. The resulting solution is heated at 50 C overnight.
Excess
benzaldehyde may be added to drive the reaction to completion. The reaction
mixture
is taken up in EtOAc and washed with saturated NaHCO3, brine, and dried
(Na2SO4)
to obtain 5 that is further purified by flash chromatography.
Example 2: Synthesis of PPAT inhibitor 2-(4-(2H-tetrazol-5-yl)benzyl)-1-(2,3-
dichlorophenyl) -2,3,4,9-tetrahydro-1 H-pyrido [3,4-b ] indole:
/_~ QNJZXCa' NH b~~ / N
NH 2 H H N N
H CI / CI / CI
CI CI \ 2 CI 3
Reagents and Conditions: a) 2,3-dichlorobenzaldehyde, TFA, DCE, heat. b) 3-
cyanobenzaldehdye, AcOH,
DCE, then NaBH(OAc)3. c) NaN3, ZnBr2, heat.
To a stirred solution of tryptamine (3.2g, 20 mmol) in dichloroethane (100
mL) was added 2,3-dichlorobenzaldehdye (3.5g, 20mmol), followed by TFA
(0.5mL).
The resulting solution was heated at reflux overnight. After concentration, a
formed
CA 02707442 2010-05-28
WO 2009/102377 PCT/US2008/084832
solid was filtered, washed with hexane, and dried to give 1 as a pale yellow
solid in
quantitative yield.
To a screw-capped 15 mL vial 1 (316 mg, 1.0 mmol), DMF (5 mL), 4-
cyanobenzaldehdye (300mg, 2.3 mmol), and AcOH (200 L) was added at ambient
temperature. To this solution was added NaBH(OAc)3 (640 mg, 3 mmol). The
resulting solution was heated at 50 C overnight. To the solution was added
additional 4-cyanobenzaldehdye (200mg, 1.5 mmol) and NaBH(OAc)3 (210 mg,
1mmol). After heating at 50 C overnight, the solution was taken up into with
EtOAc
(50 mL). The organic solution was washed with saturated NaHCO3 (25 mL), brine
(10 mL), and dried (Na2SO4) to obtain 3 (260mg, 60%) as a white solid after
purification by flash chromatography (acetone : hexane = 20: 80). iH NMR
(400MHz, CDC13) 8 2.70 (m, 1H), 2.83 (m, 2H), 3.05 (dt, 1H), 3.60 and 3.86
(two d,
2H, J = 14Hz), 5.37 (s, 1H), 7.1-7.6 (set of m, 11H); LGMS ES- 430 (M-1); >95%
pure
To a 15 mL screw-capped vial was placed 2 (140mg, 0.32 mmol), followed by
MeOH (5 mL). To this was added NaN3 (150mg, 2.5 mmol), followed by ZnBr2
(225mg, 1 mmol). The suspension was heated at 100 C overnight. Additional
NaN3
(150mg, 2.5 mmol) was added followed by heating at 100 C overnight. After
concentration, the residue was triturated with IN HC1, followed by CHC13, and
dried
to provide a solid, which was purified by flash chromatography (EtOAc) to
obtain 3
(100mg, 70%) as a yellow solid. 1H NMR (400MHz, DMSO-d6) 8 2.61 and 2.85 (two
m, 2H + 2H), 3.64 and 3.80 (two d, 2H J = 13.6Hz), 5.31 (s, 1H), 6.9-8.0 (set
of m,
11H): LGMS ES- 473 (M-1), ES+ 475 (M+1), >95% pure
Example 3: Synthesis of PPAT inhibitor 1-(3-(1H-tetrazol-5-yl)phenyl)-2-(2,3-
dichlorobenzyl) -2,3,4,9-tetrahydro-1 H-pyrido [3,4-b ] indole
a
C
_ NH c H2 a- NH b N N
H
Q701 N H
N N H H
H H N,N N,N
CN 2 N-N 3 N-N
I/ I/
Reagents and Conditions: a) 3-cyanobenzaldehdye, TFA, DCE, heat. b) NaN3,
ZnBr2, heat.
c) 2,3-dichlorobenzaldehyde, AcOH, DCE, then NaBH(OAc)3.
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To a stirred solution of tryptamine (1.60g, 10 mmol) in dichloroethane (50
mL) was added 3-cyanobenzaldehdye (1.31g, 10mmol), followed by TFA (0.25mL).
The resulting solution was heated at reflux overnight. After concentration,
the solid
was isolated on a filter, washed with hexane, and dried to give 1 as a pale
yellow solid
in quantitative yield. iH NMR (400MHz, DMSO-d6) 8 2.87 (m, 2H), 3.17 (m, 2H),
5.52 (s, 1H), 7.0-7.7 (set of m, 8H), 10.65 (s, 1H); LC/MS; ES+ 274 (M+1),
>95%
pure.
To three screw-capped 15 mL vials were placed 1 (450mg/each, 1.7
mmol/each), followed by n-BuOH/H20 (3 m/3 mL each). To this was added NaN3
(130mg, 2.0 mmol), followed by ZnBr2 (450mg, 2 mmol). The suspension was
heated at 130 C overnight. After addition of H2O and hexane, the solid was
was
isolated on filter and dried to provide 2 (1.50g total, 95%) as white solid.
1H NMR
(400MHz, DMSO-d6) 8 0.83 (t, 1H, J = 7.2Hz), 1.27 (m, 1H), 2.80 (m, 2H), 3.18
(m,
2H), 5.45 (s, 1H), 6.9-8.0 (set of m, 8H), 10. 60 (s, 1H); ES+ 317 (M+1), ES-
315 (M-
1), >95% pure.
To a screw-capped 15 mL vial was placed 2 (160 mg, 0.5 mmol), followed by
DMF/DCM (2 mL/6 mL), 2,3-dichlorobenzaldehdye (153mg, 0.9 mmol), and AcOH
(200 L) at ambient temperature. To this solution was added NaBH(OAc)3 (250
mg,
1.2 mmol). The resulting solution was heated at 40 C overnight. The solution
was
poured into H2O (20 mL) to form a solid, which was collected, washed with
hexane,
and dried to obtain 3 (130mg, 55%) as a yellow solid, after purification by
chromatography (DCM: MeOH = 95:5). 1H NMR (400MHz, CD3OD) 8 3.16 (m,
2H), 3.35 and 3.60 (two m, 2H), 4.33 (ABq, 2H, J = 14.4Hz), 5.63 (s, 1H), 7.0-
8.1 (set
of m, 11H); LC/MS ES+ 475 (M+1) ES- 473 (M-1) >95% pure
Example 4: Bacteria are dependent on PPAT, a general target for antibiotics
The gene for PPAT, named coaD (alternatively, kdtE), has been identified: see
Geerlof, et al., "Purification and characterization of Phosphopantetheine
Adenylyltransferase from E. Coli" J. Biol. Chem., 1999, 274(38), pp. 27105-11,
the
entire teachings of which are incorporated herein by reference. The gene
sequence
has been searched in a range of bacteria and in mammals using BLAST (Basic
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Local Alignment Search Tool, available online at
http://www.ncbi.nkri.nih.gov/BLAST/). The results are provided in Table 2.
Table 2: Conservation of PPAT gene (coaD) among range of bacterial species
Bacteria Gram p/n P(N) % Identity % Similarity
Klebsiella pneumoniae negative 1.4E-72 85 91
Pseudomonas aeruginosa negative 7.20E-49 61 81
Neisseria meningitides negative 4.80E-27 35 62
Enterococcusfaecium positive 4.20E-36 46 67
Staphylococcus aureus positive 2.10E-36 46 69
Staphylococcus positive 1.10E-35 44 67
Streptococcus positive 2.60E-26 36 61
(mammalian) NA - 18 -
PPAT is seen to be highly conserved across a range of bacterial pathogens.
Thus, PPAT is a general target for antibiotics. Furthermore, although PPAT is
present
in mammalian cells, the mammalian sequence is sufficiently different to
indicate that
the disclosed PPAT inhibitors can be selective for bacterial PPAT.
The gene for PPAT, coaD, is disrupted from a range of bacteria by allelic
exchange; see, for example, Geerlof, et al., above, and Freiberg, et al. 2001.
"Identification of novel essential Escherichia coli genes conserved among
pathogenic
bacteria" J Mol Microbiol Biotechnol 2001, 3, pp 483-9, the entire teachings
of which
are incorporated herein by reference. The survival of Escherichia coli,
Bacillus
subtilis, Staphylococcus aureus, and Streptococcus pneumoniae in complex
growth
media is studied. The inability of the modified bacteria to survive without
the coaD
gene indicates that PPAT is necessary for bacterial survival and is thus a
potential
antibiotic target.
An additional experiment can test the survival of Escherichia coli in media
containing exogenous dePhospho-CoA and/or CoA. Mammalian, including human
cells, can make CoA from pantothenate (vitamin B5) scavenged from the
environment. Thus, it is possible that in a human subject, human cells/tissues
could
supply CoA to a bacterium that is unable to synthesize CoA. The inability of
modified
Escherichia coli to survive in media containing exogenous dePhospho- CoA
and/or
CoA further indicates that PPAT can be an antibacterial target.
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Example 5: Kinetic assay of PPAT inhibition
The IC50 (Inhibition Concentration at 50 percent) values for the disclosed
compounds against PPAT can be determined with various concentrations of the
compounds in a range of 0.003 - 200 g/ml. Compounds with ICso values >200 can
have a measurable IC50 using a different assay method. These inhibition assays
can
be performed in 96-well assay plates, using a similar method to the screening
assay
above. The reaction buffer should contain 20mM Hepes (pH 7.5),100mM NaCl,
1mM MgC12, 0.5mM DTT, 0.006% Brij 35, 10% Glycerol, 25 M PPT, 0.5mM ATP,
0.2 Unit of pyrophosphatase, 200ng of PPAT in a total volume of 1O0 1. The
reaction
is performed for 2 minutes, and then stopped with 150m1 Malachite Green
reagent.
Absorption at 650nm is measured after 10 minutes of color development. The
IC50's
are determined with fitting data to the four-parameter method using XLfit (ID
Business Solutions Inc., Cambridge, MA). The IC50 value is derived from the
curve
as the compound concentration that gives 50% inhibition of the enzymatic
reaction.
In order to perform the IC50 assays, purified PPAT is needed. The E. coli
PPAT gene is cloned into the pET28a expression vector (Novagen, Inc., Madison,
WT) and expressed in E. coli BL21(DE3) cells. A chromatographic purification
procedure employs Q-sepharose, gel filtration, and MonoQ chromatography, as
follows. The methods are described in detailed in Geerlof, et al., above.
Each cell pellet is suspended in a 4 fold-volume of lysis buffer (50mM
KH2PO4 pH 8.0,100mM NaCl, 2mM EGTA, and 10% glycerol. Cells are broken by
passage through a Microfluidics cell disrupter 4 times, and the cell lysate
should be
centrifuged at 3,000 g for 20 minutes. The supernatant is then applied to a
pre-
equilibrated Q-sepharose column (10mM Tris-HC1 pH 8.0, 0.1mM EGTA, 1mM
PMSF,100mM NaCl, 10% glycerol, 0.1% p-mercaptoethanol, and 0.02% Brij 35).
PPAT is eluted with NaCl gradient (0.1--1M) in the equilibrium buffer. The
major
peak fractions are pooled and concentrated, then applied to a Sephacryl S200
HR
column (10mM Tris-HC1 pH 7.5, 150mM NaCl, 0.1mM EGTA, 0.1mM PMSF, 10%
glycerol, 0.1% (3-mercaptoethanol, and 0.02% Brij 35). PPAT is eluted with the
same
buffer. The major peak fractions are pooled and loaded on a pre-equilibrated
MonoQ
column (10mM Tris-HCI, pH 7.0, 0.1mM EGTA, 0.1mM PMSF, 10% glycerol, 0.1%
(3-mercaptoethanol, and 0.02% Brij 35). PPAT should be eluted with a gradient
of
NaCl from 100mM up to 1000mM. The peak fractions are pooled and dialyzed in
the
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storing buffer (10mM MOPS pH7.0, l5OmM NaCl, 0.1mM EGTA, 50% glycerol,
0.02% Brij 35), then stored at -20 C. Data for these experiments for the
compounds
of the invention are shown in Table 3.
Table 3: IC50 data for PPat inhibitors of formula I
Compound PPAT E coli (gW)
1 >200
2 >200
3 75-150
4 1-10
>200
6 >200
7 NA
8 NA
9 NA
>200
11 75-100
12 40-120
13 30-50
14 20-40
25-75
16 30-70
17 20-40
18 50-80
19 30-50
20-40
21 30-60
22 5-15
23 110-180
24 20-40
90-120
26 70-90
27 60-110
28 >200
29 >200
20-50
31 140-180
32 5-10
33 50-80
34 30-50
30-50
36 90-100
37 120-170
38 75-160
39 80-110
>200
41 90-130
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42 125-160
43 >200
44 110-160
45 >200
46 110-140
47 >200
48 20-40
49 20-30
50 20-30
51 40-60
52 80-110
53 30-50
54 >200
55 120-150
56 140-160
57 110-130
58 >200
59 >200
60 30-50
61 30-50
62 40-60
63 30-50
64 30-50
65 120-140
66 50-70
67 30-50
68 200
69 30-50
70 40-60
71 <1
72 1-10
73 >200
74 40-60
75 70-90
76 50-70
77 100-120
78 60-80
79 >200
80 30-50
81 30-50
82 >200
83 >200
84 >200
85 >200
86 >200
87 >200
88 >200
89 110-130
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90 >200
91 >200
92 20-40
93 40-60
94 100-120
95 >200
96 50-70
97 >200
98 40-60
99 >200
100 >200
101 110-130
102 90-110
103 >200
104 90-110
105 >200
106 >200
107 >200
Example 6: Measuring disclosed PPAT inhibitors' antibiotic activity against
drug-resistant bacteria
Potency, spectrum, target specificity and serum effect is evaluated by
measuring the MIC (Minimum Inhibitory Concentration). This is the lowest
concentration, in g/mL, in a series of 2-fold dilutions of the compound that
completely inhibits growth, for a panel of pathogenic bacteria. The strains
comprising
the bacterial panel are either obtained from American Type Culture Collection
(ATCC, Manassas, VA), or genetically engineered to express varying levels of
PPAT.
The ATCC strains include the following: Escherichia coli (ATCC 35218),
Staphylococcus aureus (ATCC 700699), and Enterococcusfaeciim (ATCC 700221).
Other strains include Staphylococcus aureus RN4220, Escherichia coli WO-0159,
Escherichia coli WO-0153, and Bacillus subtilis BD170 with endogenous PPAT
disrupted and complemented with PPAT under the regulation of inducible
promoter,
Pspace=
The MIC assays are performed essentially as described in the NCCLS
recommendations, the entire teachings of which are incorporated herein by
reference
(National Center for Clinical Laboratory Standards, 1997, (Methods for
Dilution
Antimicrobial Susceptibility Tests for Bacteria the Grow Aerobically), 4th
ed.;
approved standard. NCCLS document M7-A4. NCCLS, Wayne, PA.), with the
following exceptions: both Tryptic Soy broth, and Mueller Hinton broth with
and
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without the presence of serum are used as the growth medium. The concentration
range tested is from 200 to 0.39 mcg/ml. Concentrations of 50-fold the desired
final
concentration are made by 2-fold serial dilutions in 96-well microtiter
plates, after
which 2 L are transferred to the assay plates. Cells are grown up in the
appropriate
culture media and diluted back to final OD600 of 0.001, after which 98 L is
inoculated into the assay plates. The final volume in each assay well is 100
uL. After
an overnight incubation at 37 C, the assay plates are read. The MIC is
determined as
the minimal concentration that results in >80% inhibition of growth.
GOVERNMENT SUPPORT
This invention was made with government support from the National Institutes
of Health. The government has certain rights in the invention.
53
