mode of action: the inactive form of ABL is stabilized in an autoinhibited closed
conformation, where a myristoylated N-terminal residue binds to the allosteric
myristate cleft of the kinase domain (Fig. 7b) [127]. In the BCR-ABL fusion protein,
which drives tumourigenesis in a subtype of chronic myelogenous leukaemia (CML)
and acute lymphoblastic leukaemia (ALL), the autoinhibitory function of the
kinase is lost due to the fusion with BCR, resulting in constitutive activation
[128]. GNF-2 mimics the myristate residue disrupting the kinase catalytic
function by inducing this inactive state [129]. Structural comparisons showed
that the overall conformation is very similar to the native autoinhibition state of
ABL, as the N-terminal αI-helix is rotated ~90
inwards upon binding of GNF-2
and assembles the SH2 and SH3 domain [126, 130, 131]. In the active state, this
αI-helix normally adopts an extended conformation, which was exemplified by
the use of allosteric agonists [132]. Interestingly, GNF-2 binding can take place
simultaneously with inhibitors targeting the ATP-binding pocket, such as the ATP
competitive inhibitors nilotinib, erlotinib or imatinib. Numerous reports in oncology
have therefore highlighted the benefits of a combinatorial drug therapy using ATP
competitive inhibitors together with type-IV inhibitors as this treatment strategy
reduces the risk of drug-inactivating resistance mutations [126]. A promising novel
allosteric type-IV BCR-ABL inhibitor asciminib (ABL001) has now entered clinical
testing. The compound binds similar to GNF-2 to the myristate pocket of BCR-ABL,
therefore interrupting the catalytic function of this constitutively active kinase
[133, 134].
Besides the myristate pocket, also other allosteric pockets in the kinase
domain have been targeted by allosteric inhibitors. Non-ATP competitive
allosteric inhibitors of checkpoint kinase 1 (CHK1) such as the thioquinazolinones
target an allosteric site adjacent to the αD-helix. As this pocket normally serves
as a substrate recognition site of CHK1-activating kinases, the kinase cannot
Fig. 7 Examples of binding modes of type-III and type-IV inhibitors. (a) Complex of refametinib
(green) with MEK1. The inhibitor binds adjacent to the ATP site making hydrophilic interactions
with ATP (orange) (PDB: 3E8N). (b) Induced changes by the type-IV inhibitor GNF-2. Structural
changes of helix I are indicated (PDB: 3K5V and 3KF4). The insert shows the closed autoinhibited
conformation of the ABL catalytic domain interacting with the flanking SH2 and SH3 domains. The
location of the type-IV binding site is indicated (PDB: 1OPL)
Function, Structure and Topology of Protein Kinases
15
conformation, where a myristoylated N-terminal residue binds to the allosteric
myristate cleft of the kinase domain (Fig. 7b) [127]. In the BCR-ABL fusion protein,
which drives tumourigenesis in a subtype of chronic myelogenous leukaemia (CML)
and acute lymphoblastic leukaemia (ALL), the autoinhibitory function of the
kinase is lost due to the fusion with BCR, resulting in constitutive activation
[128]. GNF-2 mimics the myristate residue disrupting the kinase catalytic
function by inducing this inactive state [129]. Structural comparisons showed
that the overall conformation is very similar to the native autoinhibition state of
ABL, as the N-terminal αI-helix is rotated ~90
inwards upon binding of GNF-2
and assembles the SH2 and SH3 domain [126, 130, 131]. In the active state, this
αI-helix normally adopts an extended conformation, which was exemplified by
the use of allosteric agonists [132]. Interestingly, GNF-2 binding can take place
simultaneously with inhibitors targeting the ATP-binding pocket, such as the ATP
competitive inhibitors nilotinib, erlotinib or imatinib. Numerous reports in oncology
have therefore highlighted the benefits of a combinatorial drug therapy using ATP
competitive inhibitors together with type-IV inhibitors as this treatment strategy
reduces the risk of drug-inactivating resistance mutations [126]. A promising novel
allosteric type-IV BCR-ABL inhibitor asciminib (ABL001) has now entered clinical
testing. The compound binds similar to GNF-2 to the myristate pocket of BCR-ABL,
therefore interrupting the catalytic function of this constitutively active kinase
[133, 134].
Besides the myristate pocket, also other allosteric pockets in the kinase
domain have been targeted by allosteric inhibitors. Non-ATP competitive
allosteric inhibitors of checkpoint kinase 1 (CHK1) such as the thioquinazolinones
target an allosteric site adjacent to the αD-helix. As this pocket normally serves
as a substrate recognition site of CHK1-activating kinases, the kinase cannot
Fig. 7 Examples of binding modes of type-III and type-IV inhibitors. (a) Complex of refametinib
(green) with MEK1. The inhibitor binds adjacent to the ATP site making hydrophilic interactions
with ATP (orange) (PDB: 3E8N). (b) Induced changes by the type-IV inhibitor GNF-2. Structural
changes of helix I are indicated (PDB: 3K5V and 3KF4). The insert shows the closed autoinhibited
conformation of the ABL catalytic domain interacting with the flanking SH2 and SH3 domains. The
location of the type-IV binding site is indicated (PDB: 1OPL)
Function, Structure and Topology of Protein Kinases
15