Structural Basis of Substrate Methylation and Inhibition of SMYD2 Andrew D. Ferguson, Nicholas A. Larsen, Tina Howard, Hannah Pollard, Isabelle Green, Christie Grande, Tony Cheung, Renee Garcia- Arenas, Scott Cowen, Jiaquan Wu, Robert Godin, Huawei Chen, Nicholas Keen  Structure  Volume 19, Issue 9, Pages 1262-1273 (September 2011) DOI: 10.1016/j.str.2011.06.011 Copyright © 2011 Elsevier Ltd Terms and Conditions

Figure 1 Discovery of AZ505 (A) HTS and hit validation cascade. (B) AlphaScreen technology. (C) Dose response curve for AZ505. (D) AZ505 chemical structure. (E) Selectivity profile of AZ505. See also Figure S1. Structure 2011 19, 1262-1273DOI: (10.1016/j.str.2011.06.011) Copyright © 2011 Elsevier Ltd Terms and Conditions

Figure 2 Biophysical Characterization of AZ505 (A) ITC data showing AZ505 binding to SMYD2. (B) Kinetic analysis of AZ505 binding to SMYD2. Duplicate data points were averaged and subtracted from radiolabeled SAM background counts at each SAM concentration. Normalized counts were converted to reaction product concentrations by a standard curve of measured counts per second for known molar quantities of radiolabeled SAM, ensuring that the measured range is sufficiently broad to cover the expected counts from the experimental data. To confirm the accuracy of this method, a standard curve of measured counts for varying molar quantities of radiolabeled p53 product peptide, producing <2-fold difference in slope. See also Figure S2 and Table S1. Structure 2011 19, 1262-1273DOI: (10.1016/j.str.2011.06.011) Copyright © 2011 Elsevier Ltd Terms and Conditions

Figure 3 Overall Structure (A) The view is given directly above the pronounced surface groove that separates the N- and C-terminal lobes of SMYD2. (B) The view has been rotated by 90°. The S-sequence is cyan; the MYND domain is red; the I-SET domain is blue; the core SET domain is green; the post-SET domain is orange; and the C-terminal domain is yellow. Three coordinated zinc ions are shown as purple spheres. The cofactor SAM has white carbon atoms, red oxygen atoms, blue nitrogen atoms, and orange sulfur atoms. Structure 2011 19, 1262-1273DOI: (10.1016/j.str.2011.06.011) Copyright © 2011 Elsevier Ltd Terms and Conditions

Figure 4 Structural Comparisons (A) The human SMYD2 structure is green whereas mouse SMYD1 is cyan. (B) The human SMYD2 structure is green whereas human SMYD3 is magenta. Structure 2011 19, 1262-1273DOI: (10.1016/j.str.2011.06.011) Copyright © 2011 Elsevier Ltd Terms and Conditions

Figure 5 Cofactor and Peptide Binding Sites (A) Cofactor binding site (top) and with its molecular surface colored by electrostatic potential (bottom). (B) Close-up of the cofactor binding site. Electrostatic interactions formed between SAM and main chain and side chain atoms of SMYD2 are shown as black dashed lines. (C) The p53 peptide binding site of SMYD2 (top) and with its molecular surface colored by electrostatic potential (bottom). (D) Close-up of the p53 peptide binding site. Electrostatic interactions formed between the monomethylated p53 peptide and main chain and side chain atoms of SMYD2 are shown as black dashed lines. In these panels, the molecular surface has been colored according to electrostatic potential (calculated by APBS [Baker et al., 2001]) with blue and red corresponding to +10 kT and −10 kT, respectively. Black labels indicate SMYD2 residues whereas red labels indicate residues from the p53 peptide. Structure 2011 19, 1262-1273DOI: (10.1016/j.str.2011.06.011) Copyright © 2011 Elsevier Ltd Terms and Conditions

Figure 6 AZ505 Binding Site (A) AZ505 binding site. The final 2Fo-Fc electron density map surrounding the inhibitor is shown as blue mesh (contoured at 1σ). Water molecules are red spheres. Electrostatic interactions formed between AZ505 and main chain and side chain atoms of SMYD2 are shown as black dashed lines. (B) Electrostatic surface of the AZ505 binding site. (C) Close-up of the p53 peptide and AZ505 binding sites of SMYD2. (D) Partially overlapping binding sites. In these panels, the molecular surface has been colored according to electrostatic potential with blue and red corresponding to +10 kT and −10 kT, respectively. (E) Chemical structures of BIX-01294, E72 (a BIX-01294 analog) and AZ505. The red highlighting indicates the portion of the inhibitor that is positioned with the lysine-binding channel. Structure 2011 19, 1262-1273DOI: (10.1016/j.str.2011.06.011) Copyright © 2011 Elsevier Ltd Terms and Conditions