Supporting information

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1 Supporting information The design of a Janus Kinase 3 (JAK3) specific inhibitor 1-((2S,5R)-5-((7H-pyrrolo[2,3- d]pyrimidin-4-yl)amino)-2-methylpiperidin-1-yl)prop-2-en-1-one (PF ) allowing for the interrogation of JAK3 signaling in humans Atli Thorarensen 1 *, Martin E. Dowty 2, Mary Ellen Banker 3, Brian Juba 4, Jason Jussif 4, Lin Tsung 4, Fabien Vincent 3, Robert M Czerwinski 4, Agustin Casimiro-Garcia 1, Ray Unwalla 1, John Trujillo 5, Sidney Liang 5, Paul Balbo 4, Ye Che 5, Adam M. Gilbert 5, Matthew F. Brown 5, Matthew Hayward 5, Justin Montgomery 5, Louis Leung 2, Xin Yang 2, Sarah Soucy 4, Martin Hegen 4, Jotham Coe 5, Jonathan Langille 5, Felix Vajdos 5, Jill Chrencik 5, Jean-Baptiste Telliez 4 * 1 Worldwide Medicinal Chemistry, Pfizer Worldwide R&D, 610 Main Street, Cambridge, MA (USA). 2 Pharmacokinetics, Dynamics, and Metabolism, Pfizer Worldwide R&D, 1 Burtt Rd, Andover, MA and Eastern Point Road, Groton, CT (USA) 3 Primary Pharmacology Group, Pfizer Worldwide R&D, Eastern Point Road, Groton, CT (USA). 4 Inflammation and Immunology, Pfizer Worldwide R&D, 610 Main Street, Cambridge, MA (USA). 5 Worldwide Medicinal Chemistry, Pfizer Worldwide R&D, Eastern Point Road, Groton, CT (USA). Corresponding authors: Atli.Thorarensen@pfizer.com, : Jean-Baptiste.Telliez@pfizer.com Content Single molecular Xray for 38b Kinetics of covalent modification of on-target and off-target kinases by PF S1

2 Single Molecule X-Ray Crystallography for 38b Figure 1. Asymmetric unit with displacement parameters drawn at 50% probability Data collection was performed on a Bruker APEX diffractometer at room temperature. Data collection consisted of omega and phi scans. The structure was solved by direct methods using SHELX software suite in the Monoclinic class space group P2 1. The structure was subsequently refined by the full-matrix least squares method. All non-hydrogen atoms were found and refined using anisotropic displacement parameters. S2

3 The hydrogen atoms located on nitrogen were found from the Fourier difference map and refined with distances restrained. The remaining hydrogen atoms were placed in calculated positions and were allowed to ride on their carrier atoms. The final refinement included isotropic displacement parameters for all hydrogen atoms. Formation of HCl salt was confirmed. Analysis of the absolute structure using likelihood methods (Hooft 2008) was performed using PLATON (Spek 2010). Assuming the sample submitted is enantiopure, the results indicate that the absolute structure has been correctly assigned. The method calculates that the probability that the structure is correctly assigned is The Hooft parameter is reported as with an esd of The final R-index was 4.1%. A final difference Fourier revealed no missing or misplaced electron density. Pertinent crystal, data collection and refinement are summarized in table 8. Atomic coordinates, bond lengths, bond angles, Torsion angles and displacement parameters are listed in tables Software and References SHELXTL, Version 5.1, Bruker AXS, 1997 PLATON, A.L. Spek, J. Appl. Cryst. 2003, 36, MERCURY, C.F. Macrae, P.R. Edington, P. McCabe, E. Pidcock, G.P. Shields, R. Taylor, M. Towler and J. van de Streek, J. Appl. Cryst. 39, , OLEX2, Dolomanov, O.V.; Bourhis, L.J.; Gildea, R.J.; Howard, J.A.K.; Puschmann, H., (2009). J. Appl. Cryst., 42, R.W.W. Hooft et al. J. Appl. Cryst. (2008) S3

4 Table 1. Crystal data and structure refinement for 37b. Identification code Crystallization Empirical formula Z621 Ethanol Formula weight Temperature Wavelength Crystal system Space group P2 1 C15 H21 N2 O2 Cl 296(2) K Å Monoclinic Unit cell dimensions a = (4) Å = 90. b = (2) Å = (2). c = (4) Å = 90. Volume (5) Å 3 Z 2 Density (calculated) Mg/m 3 Absorption coefficient mm -1 F(000) 316 Crystal size x x mm 3 Theta range for data collection to Index ranges Reflections collected <=h<=12, -8<=k<=7, -13<=l<=13 Independent reflections 2492 [R(int) = ] Completeness to theta = % Absorption correction Empirical Refinement method Full-matrix least-squares on F 2 Data / restraints / parameters 2492 / 3 / 188 Goodness-of-fit on F Final R indices [I>2sigma(I)] R1 = , wr2 = R indices (all data) R1 = , wr2 = Absolute structure parameter 0.016(8) Extinction coefficient 0.024(3) Largest diff. peak and hole and e.å -3 S4

5 Table 2. Atomic coordinates ( x 10 4 ) and equivalent isotropic displacement parameters (Å 2 x 10 3 ) for 37b. U(eq) is defined as one third of the trace of the orthogonalized U ij tensor. x y z U(eq) Cl(1) 990(1) 7490(1) 6491(1) 65(1) N(1) -85(2) -1701(3) 3593(2) 42(1) N(2) 2238(2) 623(3) 3335(2) 44(1) O(1) 2751(2) 3799(3) 3414(2) 56(1) O(2) 3235(2) 2126(3) 5228(2) 54(1) C(1) -1396(2) -2514(5) 2547(3) 55(1) C(2) -994(3) -3349(5) 1543(3) 56(1) C(3) 427(2) -2498(4) 1877(2) 43(1) C(4) 1086(2) -2422(4) 3345(2) 38(1) C(5) 2382(2) -1212(4) 3992(2) 46(1) C(6) 1750(2) 514(4) 1937(2) 48(1) C(7) 363(2) -492(4) 1315(2) 45(1) C(8) 2741(2) 2297(4) 3940(2) 42(1) C(9) 3775(3) 3857(4) 5957(3) 55(1) C(10) 4710(2) 3320(4) 7332(2) 46(1) C(11) 4873(3) 4604(5) 8301(3) 60(1) C(12) 5789(3) 4197(7) 9569(3) 72(1) C(13) 6539(3) 2545(7) 9880(3) 70(1) C(14) 6375(3) 1234(6) 8921(3) 67(1) C(15) 5457(3) 1625(5) 7649(3) 54(1) S5

6 Table 3. Bond lengths [Å] and angles [ ] for 37b. N(1)-C(4) 1.500(3) N(1)-C(1) 1.501(3) N(2)-C(8) 1.342(4) N(2)-C(5) 1.459(3) N(2)-C(6) 1.467(3) O(1)-C(8) 1.213(3) O(2)-C(8) 1.349(3) O(2)-C(9) 1.436(3) C(1)-C(2) 1.528(4) C(2)-C(3) 1.521(3) C(3)-C(4) 1.525(3) C(3)-C(7) 1.528(4) C(4)-C(5) 1.509(3) C(6)-C(7) 1.508(3) C(9)-C(10) 1.503(3) C(10)-C(15) 1.381(4) C(10)-C(11) 1.384(4) C(11)-C(12) 1.385(5) C(12)-C(13) 1.357(6) C(13)-C(14) 1.388(6) C(14)-C(15) 1.387(4) C(4)-N(1)-C(1) (19) C(8)-N(2)-C(5) (18) C(8)-N(2)-C(6) 119.0(2) C(5)-N(2)-C(6) 115.7(2) C(8)-O(2)-C(9) 115.7(2) N(1)-C(1)-C(2) (18) C(3)-C(2)-C(1) 104.8(2) C(2)-C(3)-C(4) (18) C(2)-C(3)-C(7) 113.5(2) C(4)-C(3)-C(7) 110.8(2) N(1)-C(4)-C(5) 112.8(2) N(1)-C(4)-C(3) (16) C(5)-C(4)-C(3) (19) N(2)-C(5)-C(4) (18) N(2)-C(6)-C(7) (18) C(6)-C(7)-C(3) 111.9(2) O(1)-C(8)-N(2) 125.2(2) O(1)-C(8)-O(2) 123.1(2) N(2)-C(8)-O(2) 111.8(2) O(2)-C(9)-C(10) 108.6(2) C(15)-C(10)-C(11) 119.2(3) C(15)-C(10)-C(9) 121.8(2) C(11)-C(10)-C(9) 118.9(3) C(10)-C(11)-C(12) 120.2(3) C(13)-C(12)-C(11) 120.7(3) C(12)-C(13)-C(14) 119.8(3) C(15)-C(14)-C(13) 119.9(3) C(10)-C(15)-C(14) 120.2(3) S6

7 Symmetry transformations used to generate equivalent atoms: Table 4. Anisotropic displacement parameters (Å 2 x 10 3 ) for 37b. The anisotropic displacement factor exponent takes the form: -2 2 [ h 2 a* 2 U h k a* b* U 12 ] U 11 U 22 U 33 U 23 U 13 U 12 Cl(1) 104(1) 48(1) 41(1) -4(1) 32(1) -23(1) N(1) 55(1) 39(1) 38(1) 7(1) 26(1) 5(1) N(2) 49(1) 42(1) 38(1) 6(1) 16(1) -2(1) O(1) 69(1) 41(1) 59(1) 5(1) 31(1) -3(1) O(2) 63(1) 46(1) 42(1) -2(1) 13(1) -11(1) C(1) 48(1) 51(2) 68(2) 5(2) 29(1) -4(1) C(2) 60(1) 56(2) 45(1) -4(1) 17(1) -12(1) C(3) 50(1) 44(1) 36(1) -7(1) 20(1) -2(1) C(4) 47(1) 30(1) 36(1) 4(1) 18(1) 6(1) C(5) 46(1) 43(1) 40(1) 7(1) 12(1) 2(1) C(6) 54(1) 55(2) 39(1) 5(1) 24(1) -2(1) C(7) 51(1) 51(1) 30(1) 5(1) 16(1) -1(1) C(8) 39(1) 40(1) 46(1) 6(1) 19(1) 1(1) C(9) 56(1) 45(2) 53(1) -5(1) 16(1) 0(1) C(10) 38(1) 51(2) 49(1) -8(1) 20(1) -6(1) C(11) 43(1) 72(2) 65(2) -24(2) 24(1) -6(1) C(12) 50(1) 114(3) 56(2) -33(2) 27(1) -24(2) S7

8 C(13) 51(1) 105(3) 47(1) -1(2) 17(1) -20(2) C(14) 57(1) 72(2) 62(2) 12(2) 18(1) 0(1) C(15) 54(1) 56(2) 52(1) -5(1) 23(1) -1(1) Kinetics of covalent modification of on-target and off-target kinases by PF The covalent inhibitor, PF , reacts with a target kinase according to a two-step reaction (Scheme 1). According to this scheme, inhibitor potency is governed by the apparent second-order rate constant for covalent adduct formation, k inact /K i, which is composed of two elementary kinetic parameters: K i, the reversible equilibrium dissociation constant of the kinase inhibitor complex (E I), and, k inact, the rate of conversion of the (E I) complex to form the covalent adduct (E I*), also referred to as the inactivation rate. For PF inhibition of JAK3 and the kinases indicated below, the rate of the reverse of the inactivation step is very slow (less than 1 Χ 10-6 s -1 ), and thus the inactivation step is considered to be irreversible. Alternatively, if the initial (E I) complex is not capable of reaction to form a covalent adduct, then reversible inhibition via a one-step binding mechanism is possible (Scheme 2). The inactivation kinetics of PF against JAK3 or one of several off-target kinases was determined using a FRET-based assay, described in detail below. An alternative enzyme kinetic inhibition assay was employed to measure TXK kinase inhibition by PF Scheme 1. Scheme 2. PF reactivity against JAK3. To determine inhibitor potency of PF against JAK3, several TR-FRET binding experiments were performed. In the first experiment (Figure 1A), JAK3 and the on-rate probe were combined first, and subsequently mixed with a concentration series of PF (0-40 nm). Because the on-rate probe exhibits very fast dissociation, the observed decrease in TR-FRET signal is rate-limited by the binding kinetics of PF These data contain information on the overall rate of binding, k inact /K i. A series of off-rate assays was performed in which JAK3 was pre-incubated with inhibitor prior to addition of the off-rate probe. The data (e.g., Figure 2B) show that PF does not dissociate from JAK3 after addition of the probe, indicating that covalent adduct was formed during the pre-incubation period. In Figures 2B-H, the intermediate levels of TR-FRET signal reflect a combination of both free, non-inhibited, kinase and covalent adduct present at the time of probe addition (at these conditions, JAK3 concentration was in excess of PF ). In the experiments shown in Figures 2B-H, both the PF concentration and pre-incubation time were varied, enabling the time-dependence of covalent adduct (E I*) formation to be measured. Because the dissociation rate of the off-rate probe is very slow, the probe can displace non-covalently bound PF and effectively prevent further S8

9 covalent modification during the time of the assay measurement. Global analysis of all the data indicates that PF reacts with JAK3 with a k inact /K i of 3.68 Χ 10 5 M -1 s -1. PF reactivity against BTK, BLK, BMX, ITK, TEC, and TXK. Six alternative kinases (BTK, BLK, BMX, ITK, TEC, and TXK) that each contain a cysteine residue at position H10 near the ATP binding pocket were tested for their propensity to form a covalent adduct with PF In all six cases, irreversible covalent adducts were formed, but with significantly slower kinetics than were measured with JAK3. The data for BTK (Figure 3) are representative and are discussed here. In the first experiment, BTK was pre-incubated for 2 h with a concentration series of PF (0-400 nm) prior to addition of the probe. The data show that PF did not dissociate from BTK after addition of the probe, indicating that covalent adduct was formed during the pre-incubation period. The intermediate levels of TR-FRET signal observed in Figure 3A is due to incomplete formation of the BTK-PF covalent adduct during the pre-incubation time. In the experiment shown in Figure 3B, BTK was pre-incubated for 2 min with the PF concentration series (0-8 µm) prior to probe addition. Here, the initial TR-FRET value reflects the fraction of BTK present in the covalent adduct form. The gradual decrease in TR-FRET is caused by slow reaction of excess PF with initially-unreacted BTK in the presence of the probe; as the reaction progresses, the BTK-probe equilibrium is shifted from complex formation (high TR-FRET) to dissociated probe (low TR-FRET). Data for the following kinases are also presented: BLK (Figure 4), BMX (Figure 5), ITK (Figure 6), TEC (Figure 7), and TXK (Figure 8). S9

10 A B C D E F G H Figure 2. TR-FRET results for PF inactivation of JAK3. Best fit solutions to global fit of all the data are shown as smooth curves. JAK3-GST: human protein, GST-tagged (amino acids ; Life Technologies) was used at 2.14 nm final concentration in the standard assay. The conjugate antibody used was Eu-anti-GST Ab (Life Technologies). The on-rate probe used was KT178 (Life Technologies), K d = 150 nm. The off-rate probe used was KT236 (Life Technologies), K d = 0.1 nm. The following experiments were performed: (A) Standard on-rate assay using 2.85 nm JAK3, and [PF ] = 0, 0.49, 1.48, 4.44, 13.3, and 40 nm. (B) Standard off-rate assay using 2.85 nm JAK3, and [PF ] = 0, 0.66, 1.98, 5.93, 17.8, 53.3 nm. The following experiments were performed following the standard protocol: [PF ] = 0, 0.66, 1.98, 5.93, 17.8, 53.3, 160, 480 nm; pre-incubation time was (C) 30 s, (D) 60 s, and (E) 1.5 h. The following experiments were performed using the variation of the off-rate protocol: S10

11 During compound pre-incubation, [JAK3] was 28.9 nm, and [PF ] = 0, , 0.056, , 0.5, 1.5 µm; pre-incubation time was (F) 10 s, (G) 20 s, and (H) 60 s. A B Figure 3. TR-FRET results for PF inactivation of BTK. Best fit solutions to global fit of all the data are shown as smooth curves. BTK-His: human protein, His-tagged full length protein (Life Technologies) was used at 1.26 nm final concentration in the standard assay. The conjugate antibody used was Eu-anti-His Ab (Life Technologies). The probe used was KT236 (Life Technologies), K d = 30.5 nm. The following experiments were performed following the standard (on-rate) protocol: (A) [PF ] = 0, 4.9, 14.8, 44.4, 133.3, and 400 nm; pre-incubation time = 2 h. (B) [PF ] = 0, 0.5, 1.0, 2.0, 4.0, and 8.0 µm; pre-incubation time = 120 s. A B Figure 4. TR-FRET results for PF inactivation of BLK. Best fit solutions to global fit of all the data are shown as smooth curves. BLK-His: His-tagged, human full-length protein (Life Technologies) was used at 5.75 nm final concentration in the standard assay. The conjugate antibody system used was Eustreptavidin (Life Technologies) and biotin-anti-his Ab (Life Technologies). The probe used was KT236 (Life Technologies), K d = 40 nm. The following experiments were performed following the standard (on- S11

12 rate) protocol: (A) [PF ] = 0, 4.9, 14.8, 44.4, 133.3, and 400 nm; pre-incubation time = 2 h. (B) [PF ] = 0, 0.5, 1.0, 2.0, 4.0, and 8.0 µm; pre-incubation time = 120 s. A B Figure 5. TR-FRET results for PF inactivation of BMX. Best fit solutions to global fit of all the data are shown as smooth curves. BLK-His: His-tagged, human full-length protein (Life Technologies) was used at 2.0 nm final concentration in the standard assay, as defined above. The conjugate antibody system used was Eu-streptavidin (Life Technologies) and biotin-anti-his Ab (Life Technologies). The probe used was KT236 (Life Technologies), K d = 74 nm. The following experiments were performed following the standard (on-rate) protocol: (A) [PF ] = 0, 4.9, 14.8, 44.4, 133.3, and 400 nm; pre-incubation time = 2 h. (B) [PF ] = 0, 0.5, 1.0, 2.0, 4.0, and 8.0 µm; pre-incubation time = 120 s. A B Figure 6. TR-FRET results for PF inactivation of ITK. Best fit solutions to global fit of all the data are shown as smooth curves. ITK-GST: GST-tagged, human full-length protein (Life Technologies) was used at 1.82 nm final concentration in the standard assay, as defined above. The conjugate antibody used was Eu-anti-GST Ab (Life Technologies). The probe used was KT236 (Life Technologies), K d = 12.8 nm. The following experiments were performed following the standard (on-rate) protocol: (A) [PF- S12

13 ] = 0, 4.9, 14.8, 44.4, 133.3, and 400 nm; pre-incubation time = 2 h. (B) [PF ] = 0, 0.5, 1.0, 2.0, 4.0, and 8.0 µm; pre-incubation time = 120 s. A B Figure 7. TR-FRET results for PF inactivation of TEC. Best fit solutions to global fit of all the data are shown as smooth curves; the global fitting model for TEC included a linear signal drift that is proportional to the concentration of the TEC-KT178(probe) complex. This signal drift was also observed in the preliminary KT178 binding experiment performed in the absence of PF inhibitor. TEC- His: His-tagged, human full length protein (Life Technologies) was used at 7.4 nm final concentration in the standard assay, as defined above. The conjugate antibody used was Eu-anti-His Ab (Life Technologies). The probe used was KT178 (Life Technologies), K d = 1.0 nm. The following experiments were performed following the standard (on-rate) protocol: (A) [PF ] = 0, 4.9, 14.8, 44.4, 133.3, and 400 nm; pre-incubation time = 2 h. (B) [PF ] = 0, 0.5, 1.0, 2.0, 4.0, and 8.0 µm; preincubation time = 120 s. Figure 8. Inactivation of TXK kinase. The observed rates of product formation (µm formed per s), obtained from fitted TXK kinase activity data (PK/LDH coupled enzyme assay) are plotted as a function of S13

14 PF concentration. Each data set corresponds to a separate experiment conducted at a given pre-incubation time: 15 min (blue), 30 min (red), 60 min (green), 90 min (purple), 120 min (aqua). The product vs. time data were simultaneously fit to an irreversible inhibition mechanism as described in the Methods section, and the solid curves are theoretical inhibition curves (global data fitting and curve generation were performed using KinTek Explorer). S14