Kinase packing defects as drug targets

Abstract

Protein kinases constitute major targets in molecular cancer therapy. The structural conservation of kinases causes specificity problems in most drug inhibitors, often resulting in dangerous side effects. Here we survey recent approaches in drug design that exploit a molecular marker for specificity: the pattern of packing defects. These packing defects are solvent-exposed intramolecular hydrogen bonds that may be protected by drugs upon association. In this light, we review design strategies to achieve paralogue discrimination, to control cross reactivity and to overcome drug resistance induced by target mutations.

Figure 1

Specificity problems in kinase inhibition. Structural alignment (ribbon representation) of the IGF1R kinase (PDB.1K3A, ice blue), a proposed cancer target and the INSR kinase (PDB.1GAG, pink), a related target to be avoided. The degree of structural similarity between the two paralogs is staggeringly high (RMSD=1.2Å) as expected from the 80% sequence identity. The IGF1R nonconserved N1110-D1123 dehydron is also shown as a green virtual bond joining α-carbons (ρ=18 nonpolar groups for desolvation radius of 6.2Å).

Figure 2

Dehydron concept. Intramolecular backbone hydrogen bonds in target proteins (green bond) prevail only if protected from water attack. Their extent of intramolecular wrapping, ρ, is defined by counting the nonpolar groups (carbonaceous atoms, cyan) contained within the desolvation domain (grey spheres). Poorly wrapped hydrogen bonds (dehydrons) are defined with 19 or fewer hydrophobic groups in their desolvation domains (desolvation radius of 6.2Å). These packing defects consist of solvent-exposed backbone hydrogen bonds and are targetable features because of their inherent stickiness, since they promote the removal of surrounding water molecules as a mean to strengthen and stabilize the underlying electrostatic interaction.

Figure 3

Targeting non-conserved kinase packing defects. (a) Aligned backbones (ribbon representation) of Src (PDB.1BYG, ice blue), CDK2 (PDB.1AQ1, pink), Chk1 (PDB.1NVR, orange) and PDK1 (PDB.1OKY, lime) kinases complexed with staurosporine. The Src Q250-E267 dehydron (green virtual bond joining α-carbons) maps into well-wrapped backbone hydrogen bonds (grey virtual bond joining α-carbons): K65-E81 in CDK2, K69-E85 in Chk1 and K144-S160 in PDK1. Methylation at the position indicated by the yellow arrow would turn the otherwise promiscuous ligand into a wrapper of the nonconserved packing defect. (b) Aligned backbones (ribbon representation) of Abl (PDB.1FPU, ice blue) and c-Kit (PDB.1T46, pink) kinases in the induced-fit conformation generated by co-crystallyzation with imatinib. The nonconserved dehydron C673-G676 (green virtual bond joining α-carbons) in c-Kit, which aligns with the well wrapped M318-G321 hydrogen bond (grey virtual bond joining α-carbons) in Abl, could be targeted by a methylation modification of imatinib in a specific position (yellow arrow) to achieve specificity. (c) Ribbon representation of the c-Kit (PDB.1T46, ice blue) kinases in the induced-fit conformation generated by co-crystallyzation with imatinib. The F811-A814 dehydron (green virtual bond joining α-carbons) present close to the D816V mutation site could be targeted by a methylation modification of imatinib in a specific position (yellow arrow) to overcome drug resistance. (d) Aligned ATP-binding pockets (ribbon representation) of IGF1R (PDB.1K3A, backbone: ice blue, sidechains: licorice representation) and INSR (PDB.1GAG, backbone: pink, sidechains: ball-and-stick representation) kinases. The degree of structure and sequence identity is very high at the ATP binding site. However, the nonconserved dehydron N1110-D1123 (green virtual bond joining α-carbons) in IGF1R, which does not align with any well wrapped hydrogen-bond or dehydron in the INSR, could be targeted to discriminate these closely related paralogs.

Figure 3

Targeting non-conserved kinase packing defects. (a) Aligned backbones (ribbon representation) of Src (PDB.1BYG, ice blue), CDK2 (PDB.1AQ1, pink), Chk1 (PDB.1NVR, orange) and PDK1 (PDB.1OKY, lime) kinases complexed with staurosporine. The Src Q250-E267 dehydron (green virtual bond joining α-carbons) maps into well-wrapped backbone hydrogen bonds (grey virtual bond joining α-carbons): K65-E81 in CDK2, K69-E85 in Chk1 and K144-S160 in PDK1. Methylation at the position indicated by the yellow arrow would turn the otherwise promiscuous ligand into a wrapper of the nonconserved packing defect. (b) Aligned backbones (ribbon representation) of Abl (PDB.1FPU, ice blue) and c-Kit (PDB.1T46, pink) kinases in the induced-fit conformation generated by co-crystallyzation with imatinib. The nonconserved dehydron C673-G676 (green virtual bond joining α-carbons) in c-Kit, which aligns with the well wrapped M318-G321 hydrogen bond (grey virtual bond joining α-carbons) in Abl, could be targeted by a methylation modification of imatinib in a specific position (yellow arrow) to achieve specificity. (c) Ribbon representation of the c-Kit (PDB.1T46, ice blue) kinases in the induced-fit conformation generated by co-crystallyzation with imatinib. The F811-A814 dehydron (green virtual bond joining α-carbons) present close to the D816V mutation site could be targeted by a methylation modification of imatinib in a specific position (yellow arrow) to overcome drug resistance. (d) Aligned ATP-binding pockets (ribbon representation) of IGF1R (PDB.1K3A, backbone: ice blue, sidechains: licorice representation) and INSR (PDB.1GAG, backbone: pink, sidechains: ball-and-stick representation) kinases. The degree of structure and sequence identity is very high at the ATP binding site. However, the nonconserved dehydron N1110-D1123 (green virtual bond joining α-carbons) in IGF1R, which does not align with any well wrapped hydrogen-bond or dehydron in the INSR, could be targeted to discriminate these closely related paralogs.

Figure 3

Targeting non-conserved kinase packing defects. (a) Aligned backbones (ribbon representation) of Src (PDB.1BYG, ice blue), CDK2 (PDB.1AQ1, pink), Chk1 (PDB.1NVR, orange) and PDK1 (PDB.1OKY, lime) kinases complexed with staurosporine. The Src Q250-E267 dehydron (green virtual bond joining α-carbons) maps into well-wrapped backbone hydrogen bonds (grey virtual bond joining α-carbons): K65-E81 in CDK2, K69-E85 in Chk1 and K144-S160 in PDK1. Methylation at the position indicated by the yellow arrow would turn the otherwise promiscuous ligand into a wrapper of the nonconserved packing defect. (b) Aligned backbones (ribbon representation) of Abl (PDB.1FPU, ice blue) and c-Kit (PDB.1T46, pink) kinases in the induced-fit conformation generated by co-crystallyzation with imatinib. The nonconserved dehydron C673-G676 (green virtual bond joining α-carbons) in c-Kit, which aligns with the well wrapped M318-G321 hydrogen bond (grey virtual bond joining α-carbons) in Abl, could be targeted by a methylation modification of imatinib in a specific position (yellow arrow) to achieve specificity. (c) Ribbon representation of the c-Kit (PDB.1T46, ice blue) kinases in the induced-fit conformation generated by co-crystallyzation with imatinib. The F811-A814 dehydron (green virtual bond joining α-carbons) present close to the D816V mutation site could be targeted by a methylation modification of imatinib in a specific position (yellow arrow) to overcome drug resistance. (d) Aligned ATP-binding pockets (ribbon representation) of IGF1R (PDB.1K3A, backbone: ice blue, sidechains: licorice representation) and INSR (PDB.1GAG, backbone: pink, sidechains: ball-and-stick representation) kinases. The degree of structure and sequence identity is very high at the ATP binding site. However, the nonconserved dehydron N1110-D1123 (green virtual bond joining α-carbons) in IGF1R, which does not align with any well wrapped hydrogen-bond or dehydron in the INSR, could be targeted to discriminate these closely related paralogs.

Figure 3

Targeting non-conserved kinase packing defects. (a) Aligned backbones (ribbon representation) of Src (PDB.1BYG, ice blue), CDK2 (PDB.1AQ1, pink), Chk1 (PDB.1NVR, orange) and PDK1 (PDB.1OKY, lime) kinases complexed with staurosporine. The Src Q250-E267 dehydron (green virtual bond joining α-carbons) maps into well-wrapped backbone hydrogen bonds (grey virtual bond joining α-carbons): K65-E81 in CDK2, K69-E85 in Chk1 and K144-S160 in PDK1. Methylation at the position indicated by the yellow arrow would turn the otherwise promiscuous ligand into a wrapper of the nonconserved packing defect. (b) Aligned backbones (ribbon representation) of Abl (PDB.1FPU, ice blue) and c-Kit (PDB.1T46, pink) kinases in the induced-fit conformation generated by co-crystallyzation with imatinib. The nonconserved dehydron C673-G676 (green virtual bond joining α-carbons) in c-Kit, which aligns with the well wrapped M318-G321 hydrogen bond (grey virtual bond joining α-carbons) in Abl, could be targeted by a methylation modification of imatinib in a specific position (yellow arrow) to achieve specificity. (c) Ribbon representation of the c-Kit (PDB.1T46, ice blue) kinases in the induced-fit conformation generated by co-crystallyzation with imatinib. The F811-A814 dehydron (green virtual bond joining α-carbons) present close to the D816V mutation site could be targeted by a methylation modification of imatinib in a specific position (yellow arrow) to overcome drug resistance. (d) Aligned ATP-binding pockets (ribbon representation) of IGF1R (PDB.1K3A, backbone: ice blue, sidechains: licorice representation) and INSR (PDB.1GAG, backbone: pink, sidechains: ball-and-stick representation) kinases. The degree of structure and sequence identity is very high at the ATP binding site. However, the nonconserved dehydron N1110-D1123 (green virtual bond joining α-carbons) in IGF1R, which does not align with any well wrapped hydrogen-bond or dehydron in the INSR, could be targeted to discriminate these closely related paralogs.