Fig. 2: De novo design and characterization of macrocyclic binders to MCL1 and MDM2.
From: Accurate de novo design of high-affinity protein-binding macrocycles using deep learning
a, AfCycDesign prediction of MCB_D2 (purple) bound to MCL1 (gray surface). MCB_D2 side chains are shown as sticks. b, Affinity determination of MCB_D2 using SPR. SPR sensorgram from a nine-point single-cycle kinetics experiment (twofold dilution, highest concentration: 20 µM). Experimental data are shown in purple and global fits are shown with black lines. The Kd is also shown on the plot. c, Experimentally determined complex structures closely match the design model. Overlap of the X-ray crystal structure (gold and gray) with the design model for MCB_D2 (purple). The Cα r.m.s.d. for the macrocycle is 0.7 Å when the experimental structure and design models are aligned by MCL1 residues. Close-up views demonstrate strong agreement between the side-chain rotamers of the design model and the X-ray structure. d, Overlay of the macrocycle model to the crystal structure shows a Cα r.m.s.d. of 0.4 Å with nearly identical backbones and side-chain rotamers. e, Close-up view of the macrocycle-bound MCL1 structure showing the cation–π interaction at the interface. f, Close-up view of the macrocycle-bound MCL1 structure showing the hydrophobic contacts at the interface. g, AfCycDesign prediction of MDB_D8 design (blue) in complex with MDM2 (gray) shown as cartoons with interacting side chains shown as sticks, bound to MDM2 shown as surface. h, Affinity determination of MDB_D8 using SPR. SPR sensorgram from a nine-point single-cycle kinetics experiment (fivefold dilution, highest concentration: 50 µM). Experimental data are shown in blue and global fits are shown with black lines. The Kd is also shown on the plots. i, Overall and close-up views of the AfCycDesign prediction of the MDB_D8 design model, highlighting key interactions with the MDM2.
