Cryo-EM reveals an unprecedented binding site for NaV1.7 inhibitors enabling rational design of potent hybrid inhibitors
- Genentech Inc, Structural Biology, United States
- Genentech Inc, Discovery Chemistry, United States
- Genentech Inc, Neuroscience, United States
- Genentech Inc, Biochemical and Cellular Pharmacology, United States
- Genentech Inc, Drug Metabolism and Pharmacokinetics, United States
Figures
Figure 1 with 1 supplement
Structure of VSD4-NaV1.7-NaVPas.
(A) Schematic of the VSD4-NaV1.7-NaVPas channel. The portions humanized to the NaV1.7 sequence are shown in green. N-terminal domain (NTD) and CTD are indicated. (B) Side view of the single-particle …
Figure 1—figure supplement 1
Purification of VSD4-NaV1.7-NaVPas channel.
(A) VSD4-NaV1.7-NaVPas channel protein expression and purification scheme. (B) Example size-exclusion chromatogram and SDS-PAGE of nanodisc-reconstituted VSD4-NaV1.7-NaVPas channel sample.
-
Figure 1—figure supplement 1—source data 1
Source data of VSD4-NaV1.7-NaVPas purification.
- https://cdn.elifesciences.org/articles/84151/elife-84151-fig1-figsupp1-data1-v2.zip
Figure 2 with 2 supplements
Structure of GNE-3565 bound to VSD4-NaV1.7-NaVPas.
(A) Chemical structure of arylsulfonamide GNE-3565. (B, C) Top and side views of VSD4-NaV1.7-NaVPas channel bound to GNE-3565. VSD4 is highlighted in green, GNE-3565 in magenta. (D) Extracellular …
Figure 2—figure supplement 1
Cryo-EM processing workflow of GNE-3565 and GNE-9296.
(A) Data collection and processing workflow for VSD4-NaV1.7-NaVPas channel bound to GNE-3565. (B) Heat map representation of the distribution of assigned particle orientations. (C) Fourier shell …
Figure 2—figure supplement 2
Comparison of VSD4-NaV1.7 bound to the arylsulfonamides GNE-3565 and GX-936 (PDB:5EK0).
Figure 3 with 1 supplement
Structure of GDC-0310 bound to VSD4-NaV1.7-NaVPas.
(A) Chemical structure of acylsulfonamide GDC-0310. (B) Top and side views of VSD4-NaV1.7-NaVPas channel bound to GDC-0310. VSD4 is highlighted in green, GDC-0310 in magenta. (D) Extracellular view …
Figure 3—figure supplement 1
CyroEM processing workflow for GNE-1305 and GDC-0310.
(A) Example cryogenic electron microscopy (cryo-EM) micrograph image of the VSD4-NaV1.7-NaVPas channel. (B) Representative 2D-class averages of selected particles. (C) Data collection and processing …
Figure 4 with 3 supplements
Structure-based design of potent hybrid inhibitors of NaV1.7.
(A) Illustration of hybrid molecule design approach. (B) Arylsulfonamide, acylsulfonamide, and hybrid molecule poses. (C) Hybridization strategy and molecule optimization. Highlighted are molecule 2 …
Figure 4—figure supplement 1
Biophysical and pharmacological characterization of human Nav1.7 channel by using Syncropatch384.
(A) Activation and inactivation curves of Nav1.7. Activation V1/2 = –25.2 mV (95% CI: –25.8 to –24.6 mV, n = 36). Inactivation V1/2 = –66.2 mV (95% CI: –66.6 to –65.7 mV, n = 153). (B). Pharmacology …
Figure 4—figure supplement 2
Density maps of GNE-9296 and GNE-1305.
(A) The cryogenic electron microscopy (cryo-EM) map surrounding the ligand GNE-9296 (compound 2) is shown in mesh representation. (B) The cryo-EM map surrounding the ligand GNE-1305 (compound 4) is …
Figure 4—figure supplement 3
Multiple sequence alignment of human VSD4 NaV1.
1–1.9 sequences.
Videos
Video 1
Movie illustrating the quality of VSD4-NaV1.7-NaVPas channel bound to GNE-1305.
Several water molecules can be observed.
Additional files
-
Supplementary file 1
Experimental details for Cryo-EM, compound synthesis and characterization, and NaV subtype selectivity for selected NaV1.7 inhibitors.
(A) Cryogenic electron microscopy (cryo-EM) data collection, refinement and validation statistics. (B) NaV subtype selectivity for selected hybrid compounds.
- https://cdn.elifesciences.org/articles/84151/elife-84151-supp1-v2.docx
-
MDAR checklist
- https://cdn.elifesciences.org/articles/84151/elife-84151-mdarchecklist1-v2.docx
