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Contents |
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* Residue conservation analysis
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PDB id:
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Transferase
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Title:
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Human abl kinase in complex with nilotinib
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Structure:
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Proto-oncogene tyrosine-protein kinase abl1. Chain: a, b, c, d. Fragment: kinase domain (unp residues 229-500). Synonym: p150, c-abl, abelson murine leukemia viral oncogene homolog 1. Engineered: yes
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Source:
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Homo sapiens. Human. Organism_taxid: 9606. Gene: abl1, abl, jtk7. Expressed in: spodoptera frugiperda. Expression_system_taxid: 7108.
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Resolution:
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2.21Å
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R-factor:
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0.200
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R-free:
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0.242
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Authors:
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S.W.Cowan-Jacob,G.Fendrich,P.Manley,J.Liebetanz,D.Fabbro
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Key ref:
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E.Weisberg
et al.
(2005).
Characterization of AMN107, a selective inhibitor of native and mutant Bcr-Abl.
Cancer Cell,
7,
129-141.
PubMed id:
DOI:
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Date:
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09-Apr-08
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Release date:
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22-Apr-08
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PROCHECK
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Headers
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References
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Enzyme class:
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Chains A, B, C, D:
E.C.2.7.10.2
- non-specific protein-tyrosine kinase.
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Reaction:
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L-tyrosyl-[protein] + ATP = O-phospho-L-tyrosyl-[protein] + ADP + H+
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L-tyrosyl-[protein]
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+
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ATP
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=
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O-phospho-L-tyrosyl-[protein]
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+
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ADP
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+
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H(+)
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Molecule diagrams generated from .mol files obtained from the
KEGG ftp site
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DOI no:
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Cancer Cell
7:129-141
(2005)
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PubMed id:
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Characterization of AMN107, a selective inhibitor of native and mutant Bcr-Abl.
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E.Weisberg,
P.W.Manley,
W.Breitenstein,
J.Brüggen,
S.W.Cowan-Jacob,
A.Ray,
B.Huntly,
D.Fabbro,
G.Fendrich,
E.Hall-Meyers,
A.L.Kung,
J.Mestan,
G.Q.Daley,
L.Callahan,
L.Catley,
C.Cavazza,
M.Azam,
A.Mohammed,
D.Neuberg,
R.D.Wright,
D.G.Gilliland,
J.D.Griffin.
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ABSTRACT
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The Bcr-Abl tyrosine kinase oncogene causes chronic myelogenous leukemia (CML)
and Philadelphia chromosome-positive (Ph+) acute lymphoblastic leukemia (ALL).
We describe a novel selective inhibitor of Bcr-Abl, AMN107 (IC50 <30 nM),
which is significantly more potent than imatinib, and active against a number of
imatinib-resistant Bcr-Abl mutants. Crystallographic analysis of Abl-AMN107
complexes provides a structural explanation for the differential activity of
AMN107 and imatinib against imatinib-resistant Bcr-Abl. Consistent with its in
vitro and pharmacokinetic profile, AMN107 prolonged survival of mice injected
with Bcr-Abl-transformed hematopoietic cell lines or primary marrow cells, and
prolonged survival in imatinib-resistant CML mouse models. AMN107 is a promising
new inhibitor for the therapy of CML and Ph+ ALL.
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Selected figure(s)
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Figure 3.
Figure 3. Abl-AMN107 complex
A: Superposition of AMN107
(magenta) bound to Abl^M351T (orange), and imatinib (green)
bound to Abl (yellow). H bonds within the AMN107-Abl^M351T
complex are depicted as dashed red lines, whereas those in the
imatinib complex are shown in black. The variability in the
positions of side chains from the C-helix (top right corner) is
due to crystal contacts that influence the position of the
N-terminal lobe of the kinase. The methyl-imidazole group of
AMN107 packs in a hydrophobic pocket formed by these residues
with the nitrogen exposed to solvent.
B: Superposition of
parts of the backbone structures of imatinib-Abl (yellow),
AMN107-Abl^M351T (orange), and AMN107-Abl (cyan). The inhibitors
are shown in green, magenta and blue, respectively. The small
black arrows show the shifts within helix E and the preceding
loop, DE. Figure 3. Abl-AMN107 complexA: Superposition of
AMN107 (magenta) bound to Abl^M351T (orange), and imatinib
(green) bound to Abl (yellow). H bonds within the
AMN107-Abl^M351T complex are depicted as dashed red lines,
whereas those in the imatinib complex are shown in black. The
variability in the positions of side chains from the C-helix
(top right corner) is due to crystal contacts that influence the
position of the N-terminal lobe of the kinase. The
methyl-imidazole group of AMN107 packs in a hydrophobic pocket
formed by these residues with the nitrogen exposed to solvent.B:
Superposition of parts of the backbone structures of
imatinib-Abl (yellow), AMN107-Abl^M351T (orange), and AMN107-Abl
(cyan). The inhibitors are shown in green, magenta and blue,
respectively. The small black arrows show the shifts within
helix E and the preceding loop, DE.
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Figure 5.
Figure 5. Efficacy of AMN107 against 32D.p210- and
32D-E255V-Luc+ cells in vivo
Left panel: Bioluminescence of
vehicle- or AMN107-treated mice. Right panel: Quantitation of
AMN107 effects against 32D.p210-Luc+ cells in vivo. Bars are
SEM, n = 5. Figure 5. Efficacy of AMN107 against 32D.p210-
and 32D-E255V-Luc+ cells in vivoLeft panel: Bioluminescence of
vehicle- or AMN107-treated mice. Right panel: Quantitation of
AMN107 effects against 32D.p210-Luc+ cells in vivo. Bars are
SEM, n = 5.
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The above figures are
reprinted
by permission from Cell Press:
Cancer Cell
(2005,
7,
129-141)
copyright 2005.
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Figures were
selected
by an automated process.
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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T.O'Hare,
M.S.Zabriskie,
A.M.Eiring,
and
M.W.Deininger
(2012).
Pushing the limits of targeted therapy in chronic myeloid leukaemia.
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Nat Rev Cancer,
12,
513-526.
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A.Fullmer,
H.Kantarjian,
J.Cortes,
and
E.Jabbour
(2011).
New developments in the treatment of chronic myeloid leukemia and Philadelphia-positive acute lymphoblastic leukemia.
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Leuk Lymphoma,
52,
81-91.
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A.S.Corbin,
A.Agarwal,
M.Loriaux,
J.Cortes,
M.W.Deininger,
and
B.J.Druker
(2011).
Human chronic myeloid leukemia stem cells are insensitive to imatinib despite inhibition of BCR-ABL activity.
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J Clin Invest,
121,
396-409.
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A.Wolf,
P.Couttet,
M.Dong,
O.Grenet,
M.Heron,
U.Junker,
D.Ledieu,
A.Mahl,
E.Marrer,
E.Persohn,
F.Pognan,
W.Zhou,
J.Tsao,
and
D.Roman
(2011).
Preclinical evaluation of potential nilotinib cardiotoxicity.
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Leuk Res,
35,
631-637.
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B.Calabretta,
and
P.Salomoni
(2011).
Inhibition of autophagy: a new strategy to enhance sensitivity of chronic myeloid leukemia stem cells to tyrosine kinase inhibitors.
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Leuk Lymphoma,
52,
54-59.
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C.E.Vigil,
E.A.Griffiths,
E.S.Wang,
and
M.Wetzler
(2011).
Interpretation of cytogenetic and molecular results in patients treated for CML.
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Blood Rev,
25,
139-146.
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D.Bixby,
and
M.Talpaz
(2011).
Seeking the causes and solutions to imatinib-resistance in chronic myeloid leukemia.
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Leukemia,
25,
7.
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|
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E.A.Nelson,
S.R.Walker,
E.Weisberg,
M.Bar-Natan,
R.Barrett,
L.B.Gashin,
S.Terrell,
J.L.Klitgaard,
L.Santo,
M.R.Addorio,
B.L.Ebert,
J.D.Griffin,
and
D.A.Frank
(2011).
The STAT5 inhibitor pimozide decreases survival of chronic myelogenous leukemia cells resistant to kinase inhibitors.
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Blood,
117,
3421-3429.
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E.Jabbour,
J.Cortes,
and
H.Kantarjian
(2011).
Long-term outcomes in the second-line treatment of chronic myeloid leukemia: A review of tyrosine kinase inhibitors.
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Cancer,
117,
897-906.
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E.Jabbour,
M.Deininger,
and
A.Hochhaus
(2011).
Management of adverse events associated with tyrosine kinase inhibitors in the treatment of chronic myeloid leukemia.
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Leukemia,
25,
201-210.
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G.D.Demetri
(2011).
Differential properties of current tyrosine kinase inhibitors in gastrointestinal stromal tumors.
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Semin Oncol,
38,
S10-S19.
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H.J.Lee,
J.E.Thompson,
E.S.Wang,
and
M.Wetzler
(2011).
Philadelphia chromosome-positive acute lymphoblastic leukemia: current treatment and future perspectives.
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Cancer,
117,
1583-1594.
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H.M.Kantarjian,
F.J.Giles,
K.N.Bhalla,
J.Pinilla-Ibarz,
R.A.Larson,
N.Gattermann,
O.G.Ottmann,
A.Hochhaus,
J.P.Radich,
G.Saglio,
T.P.Hughes,
G.Martinelli,
D.W.Kim,
Y.Shou,
N.J.Gallagher,
R.Blakesley,
M.Baccarani,
J.Cortes,
and
P.D.le Coutre
(2011).
Nilotinib is effective in patients with chronic myeloid leukemia in chronic phase after imatinib resistance or intolerance: 24-month follow-up results.
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Blood,
117,
1141-1145.
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H.R.Mellor,
A.R.Bell,
J.P.Valentin,
and
R.R.Roberts
(2011).
Cardiotoxicity associated with targeting kinase pathways in cancer.
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Toxicol Sci,
120,
14-32.
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J.J.Powers,
J.A.Dubovsky,
P.K.Epling-Burnette,
L.Moscinski,
L.Zhang,
S.Mustjoki,
E.M.Sotomayor,
and
J.A.Pinilla-Ibarz
(2011).
A molecular and functional analysis of large granular lymphocyte expansions in patients with chronic myelogenous leukemia treated with tyrosine kinase inhibitors.
|
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Leuk Lymphoma,
52,
668-679.
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J.M.Diamond,
and
J.V.Melo
(2011).
Mechanisms of resistance to BCR-ABL kinase inhibitors.
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Leuk Lymphoma,
52,
12-22.
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J.Pinilla-Ibarz,
J.Cortes,
and
M.J.Mauro
(2011).
Intolerance to tyrosine kinase inhibitors in chronic myeloid leukemia: Definitions and clinical implications.
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Cancer,
117,
688-697.
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J.Y.Blay,
and
M.von Mehren
(2011).
Nilotinib: a novel, selective tyrosine kinase inhibitor.
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Semin Oncol,
38,
S3-S9.
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M.E.Shaker,
H.A.Salem,
G.E.Shiha,
and
T.M.Ibrahim
(2011).
Nilotinib counteracts thioacetamide-induced hepatic oxidative stress and attenuates liver fibrosis progression.
|
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Fundam Clin Pharmacol,
25,
248-257.
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M.Thomas,
W.S.Huang,
D.Wen,
X.Zhu,
Y.Wang,
C.A.Metcalf,
S.Liu,
I.Chen,
J.Romero,
D.Zou,
R.Sundaramoorthi,
F.Li,
J.Qi,
L.Cai,
T.Zhou,
L.Commodore,
Q.Xu,
J.Keats,
F.Wang,
S.Wardwell,
Y.Ning,
J.T.Snodgrass,
M.I.Broudy,
K.Russian,
J.Iuliucci,
V.M.Rivera,
T.K.Sawyer,
D.C.Dalgarno,
T.Clackson,
and
W.C.Shakespeare
(2011).
Discovery of 5-(arenethynyl) hetero-monocyclic derivatives as potent inhibitors of BCR-ABL including the T315I gatekeeper mutant.
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Bioorg Med Chem Lett,
21,
3743-3748.
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M.Y.Ho,
and
C.D.Blanke
(2011).
Gastrointestinal stromal tumors: disease and treatment update.
|
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Gastroenterology,
140,
1372-6.e2.
|
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|
|
|
|
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N.von Bubnoff,
S.P.Gorantla,
R.A.Engh,
T.M.Oliveira,
S.Thöne,
E.Aberg,
C.Peschel,
and
J.Duyster
(2011).
The low frequency of clinical resistance to PDGFR inhibitors in myeloid neoplasms with abnormalities of PDGFRA might be related to the limited repertoire of possible PDGFRA kinase domain mutations in vitro.
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Oncogene,
30,
933-943.
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P.Garland,
and
J.Apperley
(2011).
Nilotinib: evaluation and analysis of its role in chronic myeloid leukemia.
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Future Oncol,
7,
201-218.
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|
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P.Reichardt,
and
M.Montemurro
(2011).
Clinical experience to date with nilotinib in gastrointestinal stromal tumors.
|
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Semin Oncol,
38,
S20-S27.
|
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|
|
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R.A.Okimoto,
and
R.A.Van Etten
(2011).
Navigating the road toward optimal initial therapy for chronic myeloid leukemia.
|
| |
Curr Opin Hematol,
18,
89-97.
|
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|
|
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R.E.Iacob,
J.Zhang,
N.S.Gray,
and
J.R.Engen
(2011).
Allosteric interactions between the myristate- and ATP-site of the Abl kinase.
|
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PLoS One,
6,
e15929.
|
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R.Eglen,
and
T.Reisine
(2011).
Drug discovery and the human kinome: recent trends.
|
| |
Pharmacol Ther,
130,
144-156.
|
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S.Schenone,
O.Bruno,
M.Radi,
and
M.Botta
(2011).
New insights into small-molecule inhibitors of Bcr-Abl.
|
| |
Med Res Rev,
31,
1.
|
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|
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|
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T.Yoshizato,
Y.Nannya,
Y.Yoshiki,
F.Nakamura,
Y.Imai,
M.Ichikawa,
and
M.Kurokawa
(2011).
Nilotinib-induced hypothyroidism in a patient with chronic myeloid leukemia.
|
| |
Int J Hematol,
93,
400-402.
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|
|
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T.Zhou,
L.Commodore,
W.S.Huang,
Y.Wang,
M.Thomas,
J.Keats,
Q.Xu,
V.M.Rivera,
W.C.Shakespeare,
T.Clackson,
D.C.Dalgarno,
and
X.Zhu
(2011).
Structural mechanism of the Pan-BCR-ABL inhibitor ponatinib (AP24534): lessons for overcoming kinase inhibitor resistance.
|
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Chem Biol Drug Des,
77,
1.
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PDB codes:
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A.H.Wang,
Y.Y.Wang,
Y.Yao,
Z.Z.Xu,
L.Zhou,
L.Wang,
L.Zhang,
Y.Chen,
Z.X.Shen,
J.Hu,
and
J.M.Li
(2010).
Summary of 615 patients of chronic myeloid leukemia in Shanghai from 2001 to 2006.
|
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J Exp Clin Cancer Res,
29,
20.
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A.M.Carella
(2010).
Hypothesis: upfront use of ABL kinase inhibitor combination, either simultaneously or sequentially, in high-risk Ph+ leukemias?
|
| |
Ann Hematol,
89,
531-533.
|
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A.Radujkovic,
S.Fruehauf,
W.J.Zeller,
A.D.Ho,
and
J.Topaly
(2010).
Synergistic activity of nilotinib and established chemotherapeutic drugs in imatinib-sensitive and -resistant BCR-ABL-positive cells.
|
| |
Cancer Chemother Pharmacol,
66,
255-264.
|
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C.J.Lord,
and
A.Ashworth
(2010).
Biology-driven cancer drug development: back to the future.
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| |
BMC Biol,
8,
38.
|
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|
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C.Tanaka,
O.Q.Yin,
V.Sethuraman,
T.Smith,
X.Wang,
K.Grouss,
H.Kantarjian,
F.Giles,
O.G.Ottmann,
L.Galitz,
and
H.Schran
(2010).
Clinical pharmacokinetics of the BCR-ABL tyrosine kinase inhibitor nilotinib.
|
| |
Clin Pharmacol Ther,
87,
197-203.
|
|
|
|
|
|
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D.J.DeAngelo,
and
E.C.Attar
(2010).
Use of dasatinib and nilotinib in imatinib-resistant chronic myeloid leukemia: translating preclinical findings to clinical practice.
|
| |
Leuk Lymphoma,
51,
363-375.
|
|
|
|
|
|
|
E.Jabbour,
A.Hochhaus,
J.Cortes,
P.La Rosée,
and
H.M.Kantarjian
(2010).
Choosing the best treatment strategy for chronic myeloid leukemia patients resistant to imatinib: weighing the efficacy and safety of individual drugs with BCR-ABL mutations and patient history.
|
| |
Leukemia,
24,
6.
|
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|
|
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|
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E.Jabbour,
J.Cortes,
and
H.Kantarjian
(2010).
Nilotinib for the treatment of chronic myeloid leukemia: An evidence-based review.
|
| |
Core Evid,
4,
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|
E.Scott,
E.Hexner,
A.Perl,
and
M.Carroll
(2010).
Targeted signal transduction therapies in myeloid malignancies.
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| |
Curr Oncol Rep,
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E.Weisberg,
A.Ray,
R.Barrett,
E.Nelson,
A.L.Christie,
D.Porter,
C.Straub,
L.Zawel,
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I.Galinsky,
D.Frank,
A.L.Kung,
and
J.D.Griffin
(2010).
Smac mimetics: implications for enhancement of targeted therapies in leukemia.
|
| |
Leukemia,
24,
2100-2109.
|
|
|
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|
|
E.Weisberg,
H.G.Choi,
A.Ray,
R.Barrett,
J.Zhang,
T.Sim,
W.Zhou,
M.Seeliger,
M.Cameron,
M.Azam,
J.A.Fletcher,
M.Debiec-Rychter,
M.Mayeda,
D.Moreno,
A.L.Kung,
P.A.Janne,
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S.Adamia,
C.Wu,
N.Gray,
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Discovery of a small-molecule type II inhibitor of wild-type and gatekeeper mutants of BCR-ABL, PDGFRalpha, Kit, and Src kinases: novel type II inhibitor of gatekeeper mutants.
|
| |
Blood,
115,
4206-4216.
|
|
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PDB code:
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|
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|
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E.Weisberg,
X.Deng,
H.G.Choi,
R.Barrett,
S.Adamia,
A.Ray,
D.Moreno,
A.L.Kung,
N.Gray,
and
J.D.Griffin
(2010).
Beneficial effects of combining a type II ATP competitive inhibitor with an allosteric competitive inhibitor of BCR-ABL for the treatment of imatinib-sensitive and imatinib-resistant CML.
|
| |
Leukemia,
24,
1375-1378.
|
|
|
|
|
|
|
F.Fei,
S.Stoddart,
J.Groffen,
and
N.Heisterkamp
(2010).
Activity of the Aurora kinase inhibitor VX-680 against Bcr/Abl-positive acute lymphoblastic leukemias.
|
| |
Mol Cancer Ther,
9,
1318-1327.
|
|
|
|
|
|
|
F.Fei,
Y.Yu,
A.Schmitt,
M.T.Rojewski,
B.Chen,
J.Greiner,
M.Götz,
D.Bunjes,
and
M.Schmitt
(2010).
Effects of nilotinib on regulatory T cells: the dose matters.
|
| |
Mol Cancer,
9,
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|
|
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|
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F.Grimminger,
R.T.Schermuly,
and
H.A.Ghofrani
(2010).
Targeting non-malignant disorders with tyrosine kinase inhibitors.
|
| |
Nat Rev Drug Discov,
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|
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|
|
|
|
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G.Rosti,
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