How Abl ‘shape-shifts’ in drug-resistant CML

Photo from St. Jude Children’s Research Hospital

Researchers say they have determined how the structure of Abl kinase regulates its activity, enabling the enzyme to switch itself on and off.

The team believes these findings will pave the way to new treatment strategies that can overcome drug resistance in chronic myeloid leukemia (CML) and other malignancies.

Charalampos Kalodimos, PhD, of St Jude Children’s Research Hospital in Memphis, Tennessee, and his colleagues described this research in Nature Structural & Molecular Biology.

The researchers sought to understand how Abl manages to switch itself on and off by altering its shape. Abl controls this switching through allosteric regulation, in which a part of the molecule distant from its kinase domain somehow inhibits or activates Abl.

“We knew we had these 2 functional states, but we had no idea about the conditions under which Abl switched from one to another,” Dr Kalodimos said.

“We also didn’t understand how external molecules that regulate Abl acted on these 2 states. Nor did we understand how mutations that confer drug resistance affected the states.”

To investigate, the researchers used NMR spectroscopy to view Abl’s structure and watch the kinase change. The team explored how the region of Abl called the allosteric regulatory module interacted with the kinase domain to control it.

The research revealed that, in its shape-shifting, Abl was precisely balanced between its inhibition and activation states.

“We saw this very fast ‘breathing’ motion of several thousand times a second, in which the molecule goes on and off, on and off,” Dr Kalodimos said. “This motion is important because it allows other molecules that regulate Abl to adjust its activity one way or the other in a graded manner—like turning a rheostat up or down.”

Such regulation would involve pushing the Abl molecule toward either the inhibited or activated state, Dr Kalodimos said.

Newfound activator region

The researchers also discovered new details about how Abl’s structure affects its activation state. For example, the team’s experiments revealed a previously unknown activator region within Abl.

The researchers noted that the Abl regulatory module consists of 5 regions:

• An unstructured N-terminal region called the cap (residues 1–80)
• The SH3 domain (residues 85–138)
• A short linker called the connector^SH3/2 (residues 139–152), which links the SH3 and SH2 domains
• The SH2 domain (residues 153–237)
• A linker (linker^SH2–KD; residues 238–250) that connects SH2 to the kinase domain (residues 255–534).

The previously unknown activator region the researchers identified is part of the cap region comprising residues 14 to 20 (cap^PxxP), which carries a PxxP sequence motif, a preferred binding site of the SH3 domain.

The team found that cap^PxxP is an SH3-binding site that can compete with and displace the linker^SH2–KD from the SH3 domain, thereby destabilizing the inhibiting state.

The researchers said they believe the recently reported A19V drug-resistance mutation exerts its function by promoting the activated state of Abl by means of cap^PxxP.

Implications for treatment

The researchers also analyzed mutations in Bcr-Abl that allow it to become resistant to imatinib. The drug has proven effective in treating CML by plugging into the kinase domain of the over-activated Abl enzyme and shutting it down. However, in many patients, a mutation in the gene that produces Abl renders it drug-resistant.

While many of the mutations block imatinib from plugging into the kinase domain, others appear to interfere with the allosteric regulation. In effect, they may “warp” the enzyme to keep it activated.

In analyzing the structure of these allosteric mutants, Dr Kalodimos and his colleagues discovered the mutants altered Abl’s shape to activate it and did not interfere with how imatinib plugs into the kinase domain.

This finding points the way to new treatments to overcome such resistance, according to Dr Kalodimos.

“There is now a new generation of drugs that bind to the allosteric pocket to inhibit its activity,” he said. “These could be combined with [imatinib] to overcome allosteric mutations to shift Abl into an inhibited state.”

Dr Kalodimos said that treatment strategy could also be applied to other forms of leukemia that have uncontrolled Bcr-Abl activity. And this new basic understanding of Abl regulation will yield insight into similar enzymes in which allosteric regulation controls a kinase domain.

Photo from St. Jude Children’s Research Hospital

Researchers say they have determined how the structure of Abl kinase regulates its activity, enabling the enzyme to switch itself on and off.

The team believes these findings will pave the way to new treatment strategies that can overcome drug resistance in chronic myeloid leukemia (CML) and other malignancies.

Charalampos Kalodimos, PhD, of St Jude Children’s Research Hospital in Memphis, Tennessee, and his colleagues described this research in Nature Structural & Molecular Biology.

The researchers sought to understand how Abl manages to switch itself on and off by altering its shape. Abl controls this switching through allosteric regulation, in which a part of the molecule distant from its kinase domain somehow inhibits or activates Abl.

“We knew we had these 2 functional states, but we had no idea about the conditions under which Abl switched from one to another,” Dr Kalodimos said.

“We also didn’t understand how external molecules that regulate Abl acted on these 2 states. Nor did we understand how mutations that confer drug resistance affected the states.”

To investigate, the researchers used NMR spectroscopy to view Abl’s structure and watch the kinase change. The team explored how the region of Abl called the allosteric regulatory module interacted with the kinase domain to control it.

The research revealed that, in its shape-shifting, Abl was precisely balanced between its inhibition and activation states.

“We saw this very fast ‘breathing’ motion of several thousand times a second, in which the molecule goes on and off, on and off,” Dr Kalodimos said. “This motion is important because it allows other molecules that regulate Abl to adjust its activity one way or the other in a graded manner—like turning a rheostat up or down.”

Such regulation would involve pushing the Abl molecule toward either the inhibited or activated state, Dr Kalodimos said.

Newfound activator region

The researchers also discovered new details about how Abl’s structure affects its activation state. For example, the team’s experiments revealed a previously unknown activator region within Abl.

The researchers noted that the Abl regulatory module consists of 5 regions:

• An unstructured N-terminal region called the cap (residues 1–80)
• The SH3 domain (residues 85–138)
• A short linker called the connector^SH3/2 (residues 139–152), which links the SH3 and SH2 domains
• The SH2 domain (residues 153–237)
• A linker (linker^SH2–KD; residues 238–250) that connects SH2 to the kinase domain (residues 255–534).

The previously unknown activator region the researchers identified is part of the cap region comprising residues 14 to 20 (cap^PxxP), which carries a PxxP sequence motif, a preferred binding site of the SH3 domain.

The team found that cap^PxxP is an SH3-binding site that can compete with and displace the linker^SH2–KD from the SH3 domain, thereby destabilizing the inhibiting state.

The researchers said they believe the recently reported A19V drug-resistance mutation exerts its function by promoting the activated state of Abl by means of cap^PxxP.

Implications for treatment

The researchers also analyzed mutations in Bcr-Abl that allow it to become resistant to imatinib. The drug has proven effective in treating CML by plugging into the kinase domain of the over-activated Abl enzyme and shutting it down. However, in many patients, a mutation in the gene that produces Abl renders it drug-resistant.

While many of the mutations block imatinib from plugging into the kinase domain, others appear to interfere with the allosteric regulation. In effect, they may “warp” the enzyme to keep it activated.

In analyzing the structure of these allosteric mutants, Dr Kalodimos and his colleagues discovered the mutants altered Abl’s shape to activate it and did not interfere with how imatinib plugs into the kinase domain.

This finding points the way to new treatments to overcome such resistance, according to Dr Kalodimos.

“There is now a new generation of drugs that bind to the allosteric pocket to inhibit its activity,” he said. “These could be combined with [imatinib] to overcome allosteric mutations to shift Abl into an inhibited state.”

Dr Kalodimos said that treatment strategy could also be applied to other forms of leukemia that have uncontrolled Bcr-Abl activity. And this new basic understanding of Abl regulation will yield insight into similar enzymes in which allosteric regulation controls a kinase domain.

Photo from St. Jude Children’s Research Hospital

Researchers say they have determined how the structure of Abl kinase regulates its activity, enabling the enzyme to switch itself on and off.

The team believes these findings will pave the way to new treatment strategies that can overcome drug resistance in chronic myeloid leukemia (CML) and other malignancies.

Charalampos Kalodimos, PhD, of St Jude Children’s Research Hospital in Memphis, Tennessee, and his colleagues described this research in Nature Structural & Molecular Biology.

The researchers sought to understand how Abl manages to switch itself on and off by altering its shape. Abl controls this switching through allosteric regulation, in which a part of the molecule distant from its kinase domain somehow inhibits or activates Abl.

“We knew we had these 2 functional states, but we had no idea about the conditions under which Abl switched from one to another,” Dr Kalodimos said.

“We also didn’t understand how external molecules that regulate Abl acted on these 2 states. Nor did we understand how mutations that confer drug resistance affected the states.”

To investigate, the researchers used NMR spectroscopy to view Abl’s structure and watch the kinase change. The team explored how the region of Abl called the allosteric regulatory module interacted with the kinase domain to control it.

The research revealed that, in its shape-shifting, Abl was precisely balanced between its inhibition and activation states.

“We saw this very fast ‘breathing’ motion of several thousand times a second, in which the molecule goes on and off, on and off,” Dr Kalodimos said. “This motion is important because it allows other molecules that regulate Abl to adjust its activity one way or the other in a graded manner—like turning a rheostat up or down.”

Such regulation would involve pushing the Abl molecule toward either the inhibited or activated state, Dr Kalodimos said.

Newfound activator region

The researchers also discovered new details about how Abl’s structure affects its activation state. For example, the team’s experiments revealed a previously unknown activator region within Abl.

The researchers noted that the Abl regulatory module consists of 5 regions:

• An unstructured N-terminal region called the cap (residues 1–80)
• The SH3 domain (residues 85–138)
• A short linker called the connector^SH3/2 (residues 139–152), which links the SH3 and SH2 domains
• The SH2 domain (residues 153–237)
• A linker (linker^SH2–KD; residues 238–250) that connects SH2 to the kinase domain (residues 255–534).

The previously unknown activator region the researchers identified is part of the cap region comprising residues 14 to 20 (cap^PxxP), which carries a PxxP sequence motif, a preferred binding site of the SH3 domain.

The team found that cap^PxxP is an SH3-binding site that can compete with and displace the linker^SH2–KD from the SH3 domain, thereby destabilizing the inhibiting state.

The researchers said they believe the recently reported A19V drug-resistance mutation exerts its function by promoting the activated state of Abl by means of cap^PxxP.

Implications for treatment

The researchers also analyzed mutations in Bcr-Abl that allow it to become resistant to imatinib. The drug has proven effective in treating CML by plugging into the kinase domain of the over-activated Abl enzyme and shutting it down. However, in many patients, a mutation in the gene that produces Abl renders it drug-resistant.

While many of the mutations block imatinib from plugging into the kinase domain, others appear to interfere with the allosteric regulation. In effect, they may “warp” the enzyme to keep it activated.

In analyzing the structure of these allosteric mutants, Dr Kalodimos and his colleagues discovered the mutants altered Abl’s shape to activate it and did not interfere with how imatinib plugs into the kinase domain.

This finding points the way to new treatments to overcome such resistance, according to Dr Kalodimos.

“There is now a new generation of drugs that bind to the allosteric pocket to inhibit its activity,” he said. “These could be combined with [imatinib] to overcome allosteric mutations to shift Abl into an inhibited state.”

Dr Kalodimos said that treatment strategy could also be applied to other forms of leukemia that have uncontrolled Bcr-Abl activity. And this new basic understanding of Abl regulation will yield insight into similar enzymes in which allosteric regulation controls a kinase domain.