Supporting Information: Expanding the Armory: Predicting and Tuning Covalent Warhead. Reactivity.

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1 Supporting Information: Expanding the Armory: Predicting and Tuning Covalent Warhead Reactivity. Richard Lonsdale, Jonathan Burgess, Nicola Colclough, Nichola Davies, Eva M. Lenz, Alexandra L. Orton and Richard A. Ward* Chemistry and DMPK, Oncology, IMED Biotech Unit, AstraZeneca, Cambridge, UK * Richard.A.Ward@astrazeneca.com Contents Table S1. GSH t 1/2 data for compounds 1, 3 and S3 Table S2. Experimental pk a values for Compounds 3a, 8a-17a, 19a, 25a-34a, 37a, 55a-57a.... S4 Table S3. GSH t 1/2 and QM data for compounds containing a 2-chloroacetamide covalent warhead.... S5 Table S4. QM energies of compounds (E C ), Me-S adducts (E Add ), transition states (E TS ) and LUMO (E LUMO ) for All energies calculated in Hartree at the M06-2X/6-31+G(d,p)-IEF-PCM level.... S6 Figure S1. Geometries and energies of (a) transition state and (b) adduct formed during model reaction of 12 with MeS-. Calculated at the M06-2X/6-31+G(d,p)-IEF-PCM level relative to separate reactants.... S7 Figure S2. Plot of GSH half-life of aryl acrylamide compounds 8-23 against LUMO energy. Energies were calculated at the M06-2X/6-31+G(d,p)-IEF-PCM level.... S7 Figure S3. Plot of GSH half-life of aryl acrylamide compounds 3 and 8-52 against LUMO energy. Energies were calculated at the M06-2X/6-31+G(d,p)-IEF-PCM level.... S8 Figure S4. Lowest unoccupied molecular orbital (LUMO) of S8 Figure S5. Plot of GSH t 1/2 against 13 C NMR chemical shift (in ppm) for compounds 8-17 and S9 Figure S6. Plot of GSH t 1/2 against 1 H NMR chemical shift (in ppm) for compounds 8-17 and S9 Figure S7. Plot of GSH t1/2 against adduct formation energy for compounds 8-17 and 19. Energies were calculated at the M06-2X/6-31+G(d,p)-IEF-PCM level.... S10 Figure S8. Plot of measured against calculated 13 C chemical shifts for C b of compounds 8-17 and S10 S1

2 Figure S9. Plot of measured against calculated pka for compounds 3a, 8a-17a, 19a, 25a-33a, 36a and 53a-55a.... S11 Figure S10. Plot of GSH half-life of parent acrylamide X against calculated pk a of stripped acrylamide Xa for vinyl sulphonamides... S11 Figure S11. Plot of GSH t 1/2 against Hammett parameter σ ind for aromatic 6-membered 2- chloroacetamides.... S12 Cartesian coordinates [in Å] of QM optimized geometry of compound 12 (optimized at the IEF-PCM- M06-2X/6-31+G(d,p) level)... S13 Cartesian coordinates [in Å] of QM optimized geometry of the adduct of compound 12 with MeS- (optimized at the IEF-PCM-M06-2X/6-31+G(d,p) level)... S14 Cartesian coordinates [in Å] of QM optimized geometry of the transition state to adduct formation of compound 12 with MeS- (optimized at the IEF-PCM-M06-2X/6-31+G(d,p) level)... S15 References... S16 S2

3 Table S1. GSH t 1/2 data for compounds 1, 3 and Cpd SMILES GSH t 1/2 [min] 1 Fc1c(cc(cc1)Nc2ncnc3c2cc(c(c3)O[C@@H]4COCC4)NC(=O)\C=C\CN(C)C)Cl 25 3 n1(nc(c2c1ncnc2n)-c3ccc(cc3)oc4ccccc4)[c@h]5cn(ccc5)c(=o)c=c C=CC(=O)Nc1ccc(cc1)N C=CC(=O)Nc1ccc(cc1)F C=CC(=O)NCc1ccccc CN(c1ccccc1)C(=O)C=C C=CC(=O)Nc1ccccc Cc1ccccc1NC(=O)C=C COc1ccc(cc1)NC(=O)C=C C=CC(=O)Nc1ccccc1C#N C=CC(=O)Nc1cccc(c1)F Cc1ccc(cc1)NC(=O)C=C C=CC(=O)Nc1ccccn C=CC(=O)Nc1ccc(cc1)C#N CC(=C)C(=O)NC(C)(C)c1ccccc1 > CC(=C)C(=O)Nc1ccccc1 > CC(=CC(=O)Nc1ccccc1)C > C=CC(=O)Nc1ccc(cc1)N > Fc1c(cccc1Nc2ncnc3c2cc(c(c3)OC)OC4CCN(CC4)C(=O)C=C)Cl s2c1ncnc(c1cc2-c3n(cnc3-c4ccccc4)cc5n(ccc5)c(=o)c=c)n N3(CCc1c(nc(nc1)NC2CCOCC2)C3)C(=O)C=C N1([C@@H](CCC1)C(=O)Nc3c(cc2ncc(c(c2c3)Nc4cc(ccc4)CC)C(=O)N)OC)C (=O)C=C n1(ncc(c1)-c2nc(c(nc2)n)-n3nnc4c3cccc4)c5ccn(cc5)c(=o)c=c Ic1c(cc(c(c1)NCC(=O)N2CCN(CC2)C(=O)C=C)O)Cl Clc1c(cc(c(c1)NCC(=O)N2CCN(CC2)C(=O)C=C)OC)Cl N1(CCN(CC1)C(=O)C=C)c2ncc(cn2)-c3ccccc Fc1ccc(cc1)S[C@@H]2CN([C@@H](C2)C(=O)NCc3ccc(cc3)F)C(=O)C=C Clc1c(nc(nc1)Nc2c(ccc(c2)NC(=O)\C=C\CN(C)C)OC)-c3c4n(nc3)cccc Clc1ccc(cc1)C=CS(=O)(=O)N2CCN(CC2)C(=O)C=C N(C(C(O)c1cc(ccc1)OC)(C)C)C(=O)C=C S(=O)(=O)(N1C4CCC1c2c([nH]nc2-c3cc(ncc3)C)C4)C=C [nh]1nc(c2c1ccc(c2)nc(=o)c#c)-c3ccncc3 <52 39 S(=O)(=O)(Nc1ccc(cc1)NC(=O)C)C=C S(=O)(=O)(Nc1c(cccc1C)C)C=C Clc1ccc(cc1)NS(=O)(=O)C=C N(c1cnc(cc1)OC)C(=O)C#C S(=O)(=O)(N2Cc1ncccc1C2)C=C S(=O)(=O)(N1CCC(CC1)Nc2nc(ccn2)-c3n(c(nc3)C)C(C)C)C=C Fc1c(cccc1Nc2ncnc3c2cc(c(c3)OC)OC4CCN(CC4)S(=O)(=O)C=C)Cl Clc1c(cc(c(c1)OCC(=O)N2CCC(CC2)NS(=O)(=O)C=C)O)Cl Clc1c(cc(c(c1)NCC(=O)N2CCN(CC2)S(=O)(=O)C=C)OC)Cl 17.5 S3

4 48 Clc1c(cc(c(c1)NCC(=O)N2CCC(CC2)NC(=O)C#C)OC)Cl Clc1c(cc(c(c1)NCC(=O)N2CCN(CC2)C(=O)C#C)OC)Cl l N(c1onc(c1)-c2ccccc2)C(=O)C=C s1c(nc(c1)-c2ccccc2)nc(=o)c=c 4.38 Table S2. Experimental pk a values for Compounds 3a, 8a-17a, 19a, 25a-34a, 37a, 55a-57a. Cpd SMILES Exp pk a B1 Source 3a c1ccc(cc1)oc2ccc(cc2)c3c4c(ncnc4n(n3)[c@@h]5cccnc5)n 8.79 Internal 8a c1cc(ccc1n)n a c1cc(ccc1n)f a c1ccc(cc1)cn a CNc1ccccc a c1ccc(cc1)n a Cc1ccccc1N a COc1ccc(cc1)N a c1ccc(c(c1)c#n)n a c1cc(cc(c1)f)n a Cc1ccc(cc1)N a c1cc(ccc1c#n)n a COc1cc2c(cc1OC3CCNCC3)c(ncn2)Nc4cccc(c4F)Cl 9.47 Internal 25a c1ccc(cc1)c2c(n(cn2)c[c@h]3cccn3)c4cc5c(ncnc5s4)n 8.49 Internal 26a c1c2c(nc(n1)nc3ccocc3)cncc Internal 27a CCc1cccc(c1)Nc2c3cc(c(cc3ncc2C(=O)N)OC)NC(=O)[C@@H]4CC CN Internal 28a c1ccc2c(c1)nnn2c3c(ncc(n3)c4cnn(c4)c5ccncc5)n 9.08 Internal 29a c1c(c(cc(c1i)cl)o)ncc(=o)n2ccncc Internal 30a COc1cc(c(cc1NCC(=O)N2CCNCC2)Cl)Cl 7.91 Internal 31a c1ccc(cc1)c2cnc(nc2)n3ccncc Internal 32a c1cc(ccc1cnc(=o)[c@@h]2c[c@@h](cn2)sc3ccc(cc3)f)f 7.08 Internal 33a 9.45 Internal 36a CC(C)([C@H](c1cccc(c1)OC)O)N 9.25 Internal 53a c1ccc(cc1)c(c2ccccc2)n 8.15 Internal 54a c1cc2c(cc1[n+](=o)[o-])nccn Internal 55a CS(=O)(=O)c1ccc(cc1)c2ccc(nc2)N3CCNCC Internal S4

5 Table S3. GSH t 1/2 and QM data for compounds containing a 2-chloroacetamide covalent warhead. Cpd SMILES GSH t ½ [min] LUMO [Hartree] C-Cl distance [Å] 56 c1cc(ccc1nc(=o)ccl)[n+](=o)[o-] Y 57 CC(=O)c1ccc(cc1)NC(=O)CCl Y 58 c1cc(cc(c1)f)nc(=o)ccl Y 59 c1cc(ccc1nc(=o)ccl)br Y 60 Cc1ccc(cc1)NC(=O)CCl Y 61 CCOc1ccc(cc1)NC(=O)CCl Y 62 Cc1ccccc1NC(=O)CCl Y 63 c1ccc(c(c1)c(f)(f)f)nc(=o)ccl Y 64 ClCC(=O)Nc1ccc(cc1)Cl 168 nd nd nd 65 ClCC(=O)Nc1c(cccc1)C(=O)NCc2cccc c2 370 nd nd nd 66 ClCC(=O)Nc1c(cccc1)C=O 157 nd nd nd 67 FC(F)(F)c1cc(ccc1)NC(=O)CCl 155 nd nd nd 68 ClCC(=O)Nc1ccc(cc1)S(=O)(=O)NCC O 108 nd nd nd 69 [N+](=O)([O-])c1cc(ccc1)NC(=O)CCl 122 nd nd nd 70 ClCC(=O)Nc1ccc(cc1)SC 186 nd nd nd 71 ClCC(=O)Nc1ccc(cc1)CO 172 nd nd nd 72 ClCC(=O)Nc1c(cccc1)OC 321 nd nd nd 73 ClCC(=O)Nc1ccc(cc1)C(=O)N(C)C 179 nd nd nd 74 c1ccc2c(c1)ccn2c(=o)ccl N 75 c1cc(ccc1/c=c/s(=o)(=o)n2ccn(cc 2)C(=O)CCl)Cl N 76 c1ccc2c(c1)nc(nn2)nc(=o)ccl Y 77 Cc1csc(c1C#N)NC(=O)CCl Y 78 c1ccc(cc1)n2ccn(cc2)c(=o)ccl N 79 CN(Cc1ccccc1)C(=O)CCl N 80 C(C(=O)Nc1c(c(nc(c1F)F)F)F)Cl Y 81 CN(c1ccccc1)C(=O)CCl N 82 Cc1ccc(cc1NC(=O)CCl)C#N Y 83 c1ccc(cc1)nc(=o)ccl Y 84 COc1ccc(c(c1)NC(=O)CCl)OC Y 85 c1ccc(cc1)ccnc(=o)ccl Y 86 CC(C)(CNC(=O)CCl)c1ccccc Y C-Cl parallel to N-H? S5

6 Table S4. QM energies of compounds (E C ), Me-S adducts (E Add ), transition states (E TS ) and LUMO (E LUMO ) for All energies calculated in Hartree at the M06-2X/6-31+G(d,p)-IEF-PCM level. Cpd E C E Add E TS E LUMO S6

7 Figure S1. Geometries and energies of (a) transition state and (b) adduct formed during model reaction of 12 with MeS-. Calculated at the M06-2X/6-31+G(d,p)-IEF-PCM level relative to separate reactants. Figure S2. Plot of GSH half-life of aryl acrylamide compounds 8-23 against LUMO energy. Energies were calculated at the M06-2X/6-31+G(d,p)-IEF-PCM level. S7

8 Figure S3. Plot of GSH half-life of aryl acrylamide compounds 3 and 8-52 against LUMO energy. Energies were calculated at the M06-2X/6-31+G(d,p)-IEF-PCM level. Figure S4. Lowest unoccupied molecular orbital (LUMO) of 24 S8

9 Figure S5. Plot of GSH t 1/2 against 13 C NMR chemical shift (in ppm) for compounds 8-17 and 19. Figure S6. Plot of GSH t 1/2 against 1 H NMR chemical shift (in ppm) for compounds 8-17 and 19. S9

10 Figure S7. Plot of GSH t1/2 against adduct formation energy for compounds 8-17 and 19. Energies were calculated at the M06-2X/6-31+G(d,p)-IEF-PCM level. Figure S8. Plot of measured against calculated 13 C chemical shifts for C b of compounds 8-17 and 19. S10

11 Figure S9. Plot of measured against calculated pka for compounds 3a, 8a-17a, 19a, 25a-33a, 36a and 53a-55a. Figure S10. Plot of GSH half-life of parent acrylamide X against calculated pk a of stripped acrylamide Xa for vinyl sulphonamides S11

12 Figure S11. Plot of GSH t 1/2 against Hammett parameter σ ind for aromatic 6-membered 2- chloroacetamides. S12

13 Cartesian coordinates [in Å] of QM optimized geometry of compound 12 (optimized at the IEF-PCM- M06-2X/6-31+G(d,p) level) 20 Compound 12 C N C C C C C C O C C H H H H H H H H H S13

14 Cartesian coordinates [in Å] of QM optimized geometry of the adduct of compound 12 with MeS- (optimized at the IEF-PCM-M06-2X/6-31+G(d,p) level) 25 Compound 12 SMe adduct S C C C O N C C C C C C C H H H H H H H H H H H H S14

15 Cartesian coordinates [in Å] of QM optimized geometry of the transition state to adduct formation of compound 12 with MeS- (optimized at the IEF-PCM-M06-2X/6-31+G(d,p) level) 25 Compound 12 SMe transition state S C C C O N C C C C C C C H H H H H H H H H H H H S15

16 References 1. Willi, A. V., Die Substituentenwirkung der NH3+-Gruppe auf die Ionisationskonstante einer aromatischen Base. Z. Phys. Chem. 1961, 27, Biggs, A. I.; Robinson, R. A., The ionisation constants of some substituted anilines and phenols: a test of the Hammett relation. J. Chem. Soc. 1961, 0, Mayer, J. M.; Testa, B.; van der Waterbeemd, H.; Bornand-Crausaz, A., Deviations in the Log-P of Protonated Arylalkylamines and in their Apparent Log-P. Eur. J. Med. Chem. 1982, 17, Horrobin, S., The hydrolysis of some chloro-1,3,5-triazines: mechanism: structure and reactivity. J. Chem. Soc. 1963, Bolton, P. D.; Hall, F. M., Thermodynamic functions of ionization of the Anilinum and Toluidinium Ions. Australian J. Chem. 1967, 20, Willi, A. V.; Meier, W., Die Hammett'schen σ-werte der Gruppen [BOND]NH2 und [BOND]NH3+. Zwitterionen-Bildungsgleichgewichte in Lösungen aromatischer Aminosäuren. Helv. Chim. Acta 1956, 39, Vandenbelt, J. M.; Henrich, C.; Vanden Berg, S. G., Comparison of pká Values Determined by Electrometric Titration and Ultraviolet Absorption Methods. Anal. Chem. 1954, 26, Fickling, M. M.; Fischer, A.; Mann, B. R.; Packer, J.; Vaughan, J., Hammett Substituent Constants for Electron-withdrawing Substituents: Dissociation of Phenols, Anilinium Ions and Dimethylanilinium Ions. J. Am. Chem. Soc. 1959, 81, S16

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