1,228
Views
3
CrossRef citations to date
0
Altmetric
Research Paper

KRAS G12C fragment screening renders new binding pockets

ORCID Icon, ORCID Icon, ORCID Icon, ORCID Icon, ORCID Icon, ORCID Icon, ORCID Icon, ORCID Icon, ORCID Icon, ORCID Icon, , ORCID Icon, , ORCID Icon, ORCID Icon, , ORCID Icon & ORCID Icon show all
Pages 225-238 | Received 08 Jun 2021, Accepted 07 Sep 2021, Published online: 24 Sep 2021

Figures & data

Figure 1. Non-covalent fragment screening flowchart.

Figure 1. Non-covalent fragment screening flowchart.

Figure 2. Cpd1 binding mode to KRAS G12C GDP.

a) 2D structure of cpd1b Overall binding mode of cpd1. b) The ligand is in cyan. The protein overall structure is in green with switch I (as defined by [Citation40]) in orange, switch II in pink; the GDP is also depicted (in light orange) to the right of Cys12 (coloured yellow),c) Final 2FoFc-sigmaa weighted map around the ligand, contoured at 1σ,d) Superimposition of the 4EPY ligand (in magenta). .

Figure 2. Cpd1 binding mode to KRAS G12C GDP.a) 2D structure of cpd1b Overall binding mode of cpd1. b) The ligand is in cyan. The protein overall structure is in green with switch I (as defined by [Citation40]) in orange, switch II in pink; the GDP is also depicted (in light orange) to the right of Cys12 (coloured yellow),c) Final 2FoFc-sigmaa weighted map around the ligand, contoured at 1σ,d) Superimposition of the 4EPY ligand (in magenta). .

Figure 3. Covalent fragment screening flowchart.

Figure 3. Covalent fragment screening flowchart.

Figure 4. Cpd2 binding mode to KRAS G12C GDP.

a) 2D structure of cpd2 b) Overall binding mode of cpd2. Colour code as defined in c) Final 2FoFc-sigmaa weighted map around the ligand, contoured at 1σ d) Binding mode of cpd2 between the two switches (with/without surface)
Figure 4. Cpd2 binding mode to KRAS G12C GDP.

Figure 5. Cpd3 binding mode to KRAS G12C GDP.

a) 2D structure of cpd3. b) Overall binding mode of cpd3. Colour code as defined in c) Final 2FoFc-sigmaa weighted map around the ligand bound to Cys12, contoured at 1σ,d) Binding mode of cpd3 between the two switches. Dash-lines indicate putative H-bond interactions
Figure 5. Cpd3 binding mode to KRAS G12C GDP.

Table 1. Activity of the ligands

Table 2. Crystallographic data

Figure 6. Superimposition of the structure of KRAS G12C GDP in complex with cpd3 and with 4EPY ligand.

KRAS G12C GDP in complex with cpd3 is in the colour code defined in and the 4EPY structure (protein in grey, ligand in magenta) is superimposed. The dash-line represents the distance (7.4 Å) between the two ligands.
Figure 6. Superimposition of the structure of KRAS G12C GDP in complex with cpd3 and with 4EPY ligand.

Figure 7. Cpd4 binding mode to KRAS G12C GDP.

a. 2D structure of two cpd4 monomers and 2D structure of the cross-linked dimer of cpd4 bound to Cys12 b. Overall binding mode of cpd4. Colour code as defined in . Final 2FoFc-sigma weighted map around the ligand, contoured at 1σ d. Binding mode of compound 4 under Switch I
Figure 7. Cpd4 binding mode to KRAS G12C GDP.

Figure 8. Surface representation of KRAS G12C GDP in complex with cpd4.

The distal part of the dimeric cpd4 opens room for affinity optimization
Figure 8. Surface representation of KRAS G12C GDP in complex with cpd4.

Figure 9. Overall KRAS G12C structure and surface representation of the four binding pockets identified on KRAS. The orientation of the protein is the same in all pictures.

a. Overall structure of KRAS G12C (colour code as defined in Figure 2) with oval shapes identifying the four binding sites as detailed to the right and colour-coded by ligand b. Already identified Switch II binding pocket (in magenta, sotorasib, pdb code 6OIM) c. Already identified Switch I/II binding pocket (in yellow, BI-2852, pdb code 6ZL5) d. Newly identified cleft between Switch I and Switch II (cpd3, in cyan) e. Newly identified Switch I binding pocket (cpd4, in pink)
Figure 9. Overall KRAS G12C structure and surface representation of the four binding pockets identified on KRAS. The orientation of the protein is the same in all pictures.

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.