Biomedical Engineering Reference
In-Depth Information
11. 5.1 S
TRUCTURE
-B
ASED
D
ESIGN
OF
P
ROTEIN
K
INASE
I
NHIBITORS
Owing to their central roles in mediating cellular signaling pathways, protein kinases are increas-
ingly important targets for treating a number of diseases. In particular, many of the over 500 kinases
encoded by the human genome function to regulate tumor cell proliferation, migration, and sur-
vival, rendering them attractive targets for chemotherapeutic intervention in the treatment of
cancer. Despite their diversity, all protein kinases catalyze the transfer of the
-phosphate of ATP
to the hydroxyl group of serine, threonine, or tyrosine residues on specii c proteins. Their catalytic
domains rel ect this singular function in that they share a common feature called the protein kinase
fold, which includes a highly conserved ATP-binding pocket, l anked by N-terminal and C-terminal
lobes. The ATP-binding site has been the major focus of inhibitor design; owing to its high degree
of conservation, however, selectivity has been a major challenge for inhibitors that target this bind-
ing site of protein kinases. The use of biostructure-based approaches has therefore been of great
importance in the optimization of targeted anticancer therapies.
X-ray crystallographic studies have indicated that the catalytic activity in most kinases is con-
trolled by an “activation loop,” which adopts different conformations depending upon the phos-
phorylation state of serine, threonine, or tyrosine residues within the loop. In kinases that are fully
active, the loop is thought to be stabilized in an open conformation as a result of phosphorylation,
allowing a
γ
-strand within the loop to serve as a platform for substrate binding. While the “active”
conformation of the loop is very similar in all known structures of activated kinases, there is great
variability in the loop conformation in the inactive state of kinases. In this inactive-like conforma-
tion, the loop places steric constraints, which preclude substrate binding.
One of the i rst protein kinase inhibitors developed as a targeted cancer therapy is imatinib
(Gleevec
®
; Novartis Pharmaceuticals, Basel, Switzerland). Imatinib has been used with remark-
able success to treat patients with chronic myeloid leukemia (CML), which is a malignancy result-
ing from the deregulated activity of Abl due to a chromosomal translocation that gives rise to
the breakpoint cluster region-abelson tyrosine kinase oncogene (BCR-ABL). Imatinib inhibits the
tyrosine kinase activity of Bcr-Abl and it is considered as a frontline treatment for CML by virtue
of its high degree of efi cacy and selectivity. Together with biochemical studies, crystallographic
studies of the interaction of imatinib with the Abl kinase domain have revealed that imatinib binds
to the Bcr-Abl ATP-binding site preferentially when the centrally located activation loop is not
phosphorylated, thus stabilizing the protein in an inactive conformation (Figure 11.7). In addition,
imatinib's interactions with the NH
2
-terminal lobe of the kinase appear to involve an induced-i t
mechanism, further adding to the unique structural requirements for optimal inhibition. One of the
most interesting aspects of this interaction is that the specii city of inhibition is achieved despite
the fact that residues that contact imatinib in Abl kinase are either identical or very highly con-
served in other Src-family tyrosine kinases. Thus, despite targeting the relatively well conserved
nucleotide-binding pocket of Abl, studies have shown that imatinib achieves its high specii city by
recognizing the distinctive inactive conformation of the Abl activation loop. Biostructure-based
methods have had a further impact on more recent efforts to design second-generation therapies
targeting imatinib-resistant mutations in Bcr-Abl kinase that have been identii ed in CML patients.
It is very likely that these new inhibitors will have substantial clinical utility in the treatment of
imatinib-resistant CML; continued exploration of the structural details of the interactions between
these compounds and the mutant kinase are still necessary, as resistance remains an inevitable
consequence of such drug treatment regimens.
The three catalytically active receptor tyrosine kinases (RTKs) of the ErbB family represent
another attractive target for the treatment of a variety of cancers: epidermal growth factor receptor
(EGFR, also known as ErbB1), ErbB2 (also known as HER2/
neu
), and ErbB4. These RTKs are large,
multidomain proteins that contain an extracellular ligand-binding domain, a single transmembrane
domain, and a cytoplasmic domain responsible for the tyrosine kinase activity. Ligand binding to the
extracellular domain induces the formation of receptor homo- and heterodimers, which leads to
activation of the tyrosine kinase activity and subsequent phosphorylation of the cytoplasmic tail.
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