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1 SUPPORTING INFORMATION Discovery of a potent class I PRMT fragment inhibitor Renato Ferreira de Freitas 1,$, Mohammad S. Eram 1,$, Magdalena M. Szewczyk 1, Holger Steuber 2, David Smil 1, Hong Wu 1, Fengling Li 1, Guillermo Senisterra 1, Aiping Dong 1, Peter J. Brown 1, Marion Hitchcock 2, Dieter Moosmayer 2, ChrisLan M. Stegmann 2, Ursula Egner², Cheryl Arrowsmith 1,3, Dalia Barsyte- Lovejoy 1, Masoud Vedadi 1,4,*, MaUhieu Schapira 1,4,* p.1 Title page p.2 Supplementary Table 1. SelecLvity profile of compound 2b p.3 Supplementary Table 2. Crystallography data and refinement stalslcs for PRMT6 in complex with SAH and 2b (PDB code 4QPP) p.4 Supplementary Figure 1. dose- dependent inhibilon of PRMT1, PRMT3, CARM1, PRMT5, PRMT6, PRMT7 and PRMT8 with compounds 4 to 7 p.5 Supplementary Table 3. Structure factors of PRMT6- fragment 7 complex structure p.6 Supplementary Figure 2. The superposilon of the bound conformalon of fragment 7 with 2 and 3 p.7 Supplementary Figure 3. (A) SuperposiLon of PRMT6 in complex with fragment 3 and 7 p.8 Supplementary Figure 4. F o - F c omit electron density of Fragment 7 bound to the hydrophobic exosite of PRMT6 p.9 Supplementary Figure 5. Structural interpretalon of the seleclvity profile of 7 p.1 Supplementary Figure 6. Mechanism of aclon (MOA) of EPZ2411 (Compound 3) p.11 Supplementary Table 4. Formula string and aclvity of fragment 1 PRMT6 hits
2 Protein IC 5 (µm) 2b Hill slope PRMT PRMT CARM1.6.9 PRMT5 NI NA PRMT6.7.8 PRMT Supplementary Table 1 seleclvity profile of compound 2b 2
3 Supplementary Table 2: Crystallography data and refinement stalslcs for PRMT6 in complex with SAH and 2b (PDB code 4QPP) 3
4 . 1 1 P R M T 1 A c tiv ity (% ) P R M T 1 A c tiv ity (% ) P R M T 1 A c tiv ity (% ) P R M T 1 A c tiv ity (% ) C o m p o u n d 7 (m M ) Supplementary Figure 1 P R M T 3 A c tiv ity (% ) P R M T 3 A c tiv ity (% ) P R M T 3 A c tiv ity (% ) P R M T 3 A c tiv ity (% ) Dose- dependent inhibilon of PRMT1, PRMT3, CARM1, PRMT5, PRMT6, PRMT7 and PRMT8 with compounds 4 to 7 P R M T 5 A c tiv ity (% ) P R M T 4 A c tiv ity (% ) P R M T 5 A c tiv ity (% ) P R M T 4 A c tiv ity (% ) P R M T 5 A c tiv ity (% ) P R M T 4 A c tiv ity (% ) P R M T 5 A c tiv ity (% ) P R M T 4 A c tiv ity (% ) P R M T 6 A c tiv ity (% ) P R M T 6 A c tiv ity (% ) P R M T 6 A c tiv ity (% ) P R M T 6 A c tiv ity (% ) P R M T 7 A c tiv ity (% ) P R M T 7 A c tiv ity (% ) P R M T 7 A c tiv ity (% ) P R M T 7 A c tiv ity (% ) P R M T 8 A c tiv ity (% ) P R M T 8 A c tiv ity (% ) P R M T 8 A c tiv ity (% ) P R M T 8 A c tiv ity (% )
5 Supplementary Table 3: Crystallography data and refinement stalslcs of PRMT6- fragment 7 complex structure 5
6 Supplementary Figure 2. The superposilon of the bound conformalon of fragment 7 (green) with 2 (2Y1W, yellow) and 3 (4Y3, magenta) shows that the alkylamino side chain of the inhibitors align almost perfectly. For clarity the residues of the binding pocket are hidden. 6
7 (A) (B) Supplementary Figure 3. (A) SuperposiLon of PRMT6 (grey) in complex with compounds 3 (magenta) and 7 (green) shows that 3 occupies the hydrophobic shelf. For clarity, only the side chains of PRMT6-3 are shown (colored by atom type). (B) Ligand pocket surface colored by binding properles (green, hydrophobic surface; red, hydrogen bond acceptor potenlal; blue, hydrogen 7 bond donor potenlal).
8 Supplementary Figure 4. Fragment 7 (magenta) bound to the hydrophobic exosite of monomer A. The F o - F c omit electron density is shown in blue at 2.4 s. 8
9 Supplementary Figure 5. The superposilon of PRMT6 (green) in complex with fragment 7 (cyan) and PRMT3 (1F3L, yellow) indicates the possibility of a minor clash between the side chain of I226 clashes and the inhibitor. For clarity, only the residues that are different between the two enzymes are shown. 9
10 A B IC 5 (n M ) 5 IC 5 (n M ) [p e p tid e ]/K m [S A M ]/K m Supplementary Figure 6. Mechanism of acson (MOA) of EPZ2411 (Compound 3). MOA of compound 3 was assessed by determining IC 5 values for the compound at varying concentralons of (A) peplde and (B) SAM at fixed concentralons of SAM (12 μm) and peplde (2.5 μm), respeclvely. The error bars represent the standard devialon of three sets of experiments. 1
11 Supplementary Table 4. Formula string and aclvity of fragment PRMT6 hits Comp SMILES PRMT1 PRMT3 IC5 (µm) IC5 (µm) PRMT4 IC5 (µm) PRMT5 PRMT6 IC5 (µm) IC5 (µm) PRMT7 IC5 (µm) 2b CNCCN1CCC(CC1)C1=CC=C2NC(=C(Cl)C2=C1)C1=CC=CC=C1OC NI.7 ND 1.7 PRMT8 IC5 (µm) 4 CCNC(=O)C(C)N >1 >1 15 ± 7 NI >2 NI >2 5 CNCCN1CCC(C)CC1 48 ± 7 >5.2 ± NI 2.1 ±.3 NI 15 ± 1 6 CNCCN(C)C 39 ± 3 35 ± 2 3 ±.2 NI 5 ±.6 NI 7 ± NCCN1CCC(CC2=CC=CC=C2)CC1 12 ±.6 19 ± 1 1 ±.4 NI.3 ±.4 NI 2.1 ±.2 8 CN1CCCN(CC2=CC=C(CN)C=C2)CC1 24 ± 1 9 NCC1=CC(CN2CCCC2)=CC=C1 36 ± 31 1 CN(C)CC1=CC=C(CSCCN)O1 72 ± 7 11 CNCC1=CC=CC(=C1)C1=CSC=C1 69 ± 5 12 CNCC1=CC=C(C)S1 99 ± 6 13 CNCC1=CC=CC(=C1)C1=CC=NC=C1 1 ± CNCC1=CC(=CC=C1)C1=CC=CS1 125 ± CNCC1=CC=CC(=C1)C1=CC=CN=C1 14 ± 9 16 CC1=C(SC(N)=N1)N1C=CC(=N1)C(F)(F)F 46 ± 5 17 CNCC1=CC(=CC=C1)C1=CSC(C)=N1 136 ± CNCC1=CC(=CC=C1)C1=CC=CO1 146 ± NC1=CC=C(C=C1)S(=O)(=O)NC1=NC=CS1 43 ± 34 2 CNCC1=CC=CC(=C1)N1CCCCC1 17 ± 8 11
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