Supplementary Table 1. In vitro kinase selectivity of GDC-0879

Kinase Name % Activity Kinase Name % Activity Kinase Name % Activity Abl(h) 109 eEF-2K(h) 95 KDR(h) 128 Abl(m) 108 EGFR(h) 107 Lck(h) 88 Abl(T315I)(h) 98 EGFR(L858R)(h) 104 LIMK1(h) 97 ALK(h) 90 EGFR(L861Q)(h) 103 LKB1(h) 98 ALK4(h) 106 EphA1(h) 114 LOK(h) 81 AMPK(r) 94 EphA2(h) 97 Lyn(h) 112 Arg(h) 94 EphA3(h) 94 MAPK1(h) 87 Arg(m) 98 EphA4(h) 99 MAPK2(h) 91 ARK5(h) 96 EphA5(h) 80 MAPKAP-K2(h) 108 ASK1(h) 104 EphA7(h) 87 MAPKAP-K3(h) 103 Aurora-A(h) 105 EphA8(h) 96 MEK1(h) 94 Axl(h) 100 EphB1(h) 101 Met(h) 82 Blk(m) 113 EphB2(h) 103 MST1(h) 95 Bmx(h) 100 EphB3(h) 105 MST2(h) 101 p70S6K(h) 99 BRK(h) 89 EphB4(h) 94 PAK2(h) 91 BrSK1(h) 109 ErbB4(h) 111 Fer(h) 97 PAK4(h) 120 BrSK2(h) 99 Fes(h) 89 PAK6(h) 120 BTK(h) 100 FGFR1(h) 101 PDGFR-beta(h) 101 CaMKI(h) 98 FGFR2(h) 102 PDGFR-alpha(h) 120 CaMKII(r) 105 FGFR3(h) 107 PDK1(h) 99 CaMKIV(h) 104 FGFR4(h) 99 PKA(h) 97 CDK1/cyclinB(h) 105 Fgr(h) 105 PKB-beta(h) 112 CDK2/cyclinA(h) 103 Flt1(h) 98 PKB-alpha(h) 99 CDK2/cyclinE(h) 104 Flt3(D835Y)(h) 61 PKB-gamma(h) 100 CDK3/cyclinE(h) 108 Flt3(h) 103 PKC-mu(h) 112 CDK5/p25(h) 97 Flt4(h) 96 PKC-beta-I(h) 104 CDK5/p35(h) 98 Fms(h) 97 PKC-beta-II(h) 104 CDK6/cyclinD3(h) 107 Fyn(h) 107 PKC-alpha(h) 100 CDK7/cyclinH/MAT1(h) 97 GSK3-beta(h) 103 PKC-gamma(h) 116 CDK9/cyclin T1(h) 98 GSK3-alpha(h) 108 PKC-delta(h) 107 CHK1(h) 100 Hck(h) 99 PKC-epsilon(h) 103 CHK2(h) 100 HIPK1(h) 101 PKC-zeta(h) 102 CK1(y) 56 HIPK2(h) 102 PKC-eta(h) 101 CK1-delta(h) 48 HIPK3(h) 102 PKC-theta(h) 100 CK2(h) 98 IGF-1R(h) 113 PKC-iota(h) 115 CK2-alpha2(h) 89 IKK-beta(h) 110 Plk3(h) 96 cKit(D816V)(h) 102 IKK-alpha(h) 98 Ret(h) 133 cKit(h) 124 IR(h) 97 RIPK2(h) 77 c-RAF(h) 8 IRAK1(h) 94 Rsk1(h) 76 CSK(h) 116 IRAK4(h) 112 SGK(h) 103 cSRC(h) 86 IRR(h) 97 TAK1(h) 100 DAPK1(h) 101 ITK(h) 92 Tie2(h) 91 DAPK2(h) 124 JAK2(h) 107 TrkB(h) 124 DDR2(h) 101 JAK3(h) 101 ZAP-70(h) 124 DMPK(h) 95 JNK1-alpha1(h) 91 DRAK1(h) 100 JNK2-alpha2(h) 96 DYRK2(h) 95 JNK3(h) 91 Supplementary Table 2. GDC-0879 or Cmpd 2a treatment potently induces an anti-proliferative gene signature in BRAFV600E A375 melanoma cells

Gene ontology Gene ontology GDC-0879 GDC-0879 Cmpd 2a Cmpd 2a BRAF shRNA BRAF shRNA ID (EntrezGene) Name p-value change (log2) p-value change (log2) p-value change (log2) GO:0006259 DNA metabolism 4.99E-40 -4.0718 2.93E-49 -3.856395 5.55E-17 -1.293782 GO:0007049 cell cycle 9.12E-37 -3.144028 1.35E-57 -3.241422 2.57E-25 -1.221247 GO:0006260 DNA replication 1.09E-29 -4.975925 2.85E-37 -4.769656 1.57E-14 -1.59285 Supplementary Table 3. GDC-0879 treatment effectively inhibits in vivo growth of BRAFV600E human tumor xenografts BRAF KRAS % Xenograft Tumor tissue genotype genotype Inhibition LOX-IMVI Melanoma V600E WT 93 A375 Melanoma V600E WT 85 SK23 Melanoma WT WT 18 Colo205 Colon V600E WT 53 HT29 Colon V600E WT <10 HCT116 Colon WT G13D <10 HM7 Colon WT WT <10 Calu6 NSCLC WT Q61K 11 ASPC1 Pancreas WT G12D <10 Supplementary Figure 1. Multiple doses of GDC-0879 leads to sustained inhibition of tumor proliferation

AB Vehicle GDC-0879 Vehicle GDC-0879

1 hr 4 hr

4 hr 24 hr

Ki67 IHC (study day 7)

8 hr

8 hr

pERK IHC (study day 1) Supplementary Table 4. GDC-0879 treatment effectively inhibits in vivo growth of BRAFV600E primary human tumor xenografts in nude mice.

BRAF NRAS KRAS % Xenograft Tumor tissue genotype genotype genotype Inhibition MEXF 989 Melanoma V600E WT WT 98 MEXF 514 Melanoma V600E WT WT 83 MEXF 276 Melanoma V600E WT WT 95 MEXF 1341 Melanoma WT Q61K WT <10 MEXF 535 Melanoma WT Q61K WT <10 MEXF 274 Melanoma WT WT WT <10 LXFA 629 NSCLC WT WT WT <10 LXFA 983 NSCLC WT WT G12C <10 LXFA 1041 NSCLC WT WT G12V <10 Supplementary Figure 2. PK/PD relationship of PD-0325901 in KRAS-mutant HCT-116 xenograft tumors

60 250 Plasma (μmol/L) pERK/tERK 50 200

40 mol/L) μ 150

30

100

20 Plasma concentration( pERK/tERK in tumors (% control) 50 10

0 0 Hours 0.5 2 6 16 24 PD-0325901 (25 mg/kg) Supplementary Figure 3. In vitro activity of RAF and MEK inhibitors across tumor indications

A B

20 10 M) M) μ

15 μ 7.5 ( ( 50 50

10 5

5 2.5 MEK InhEC GDC-0879 EC

0 0

Colon Colon Breast Ovarian NSCLC Breast Prostate Ovarian NSCLC Prostate Melanoma Pancreatic Melanoma Pancreatic Tumor indication Tumor indication