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 8-52.... 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 56-86 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 8-23. 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 24... S8 Figure S5. Plot of GSH t 1/2 against 13 C NMR chemical shift (in ppm) for compounds 8-17 and 19.... S9 Figure S6. Plot of GSH t 1/2 against 1 H NMR chemical shift (in ppm) for compounds 8-17 and 19.... 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 19.... S10 S1
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
Table S1. GSH t 1/2 data for compounds 1, 3 and 8-52. 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 1180 8 C=CC(=O)Nc1ccc(cc1)N 816 9 C=CC(=O)Nc1ccc(cc1)F 323 10 C=CC(=O)NCc1ccccc1 2940 11 CN(c1ccccc1)C(=O)C=C 436 12 C=CC(=O)Nc1ccccc1 299 13 Cc1ccccc1NC(=O)C=C 428 14 COc1ccc(cc1)NC(=O)C=C 524 15 C=CC(=O)Nc1ccccc1C#N 37.2 16 C=CC(=O)Nc1cccc(c1)F 145 17 Cc1ccc(cc1)NC(=O)C=C 361 18 C=CC(=O)Nc1ccccn1 22 19 C=CC(=O)Nc1ccc(cc1)C#N 32.9 20 CC(=C)C(=O)NC(C)(C)c1ccccc1 >8640 21 CC(=C)C(=O)Nc1ccccc1 >10 000 22 CC(=CC(=O)Nc1ccccc1)C >10 000 23 C=CC(=O)Nc1ccc(cc1)N >10 000 24 Fc1c(cccc1Nc2ncnc3c2cc(c(c3)OC)OC4CCN(CC4)C(=O)C=C)Cl 1640 25 s2c1ncnc(c1cc2-c3n(cnc3-c4ccccc4)cc5n(ccc5)c(=o)c=c)n 1700 26 N3(CCc1c(nc(nc1)NC2CCOCC2)C3)C(=O)C=C 252 27 N1([C@@H](CCC1)C(=O)Nc3c(cc2ncc(c(c2c3)Nc4cc(ccc4)CC)C(=O)N)OC)C (=O)C=C 211 28 n1(ncc(c1)-c2nc(c(nc2)n)-n3nnc4c3cccc4)c5ccn(cc5)c(=o)c=c 949 29 Ic1c(cc(c(c1)NCC(=O)N2CCN(CC2)C(=O)C=C)O)Cl 367 30 Clc1c(cc(c(c1)NCC(=O)N2CCN(CC2)C(=O)C=C)OC)Cl 400 31 N1(CCN(CC1)C(=O)C=C)c2ncc(cn2)-c3ccccc3 691 32 Fc1ccc(cc1)S[C@@H]2CN([C@@H](C2)C(=O)NCc3ccc(cc3)F)C(=O)C=C 90.8 33 2850 34 Clc1c(nc(nc1)Nc2c(ccc(c2)NC(=O)\C=C\CN(C)C)OC)-c3c4n(nc3)cccc4 352 35 Clc1ccc(cc1)C=CS(=O)(=O)N2CCN(CC2)C(=O)C=C 283 36 N(C(C(O)c1cc(ccc1)OC)(C)C)C(=O)C=C 3160 37 S(=O)(=O)(N1C4CCC1c2c([nH]nc2-c3cc(ncc3)C)C4)C=C 49 38 [nh]1nc(c2c1ccc(c2)nc(=o)c#c)-c3ccncc3 <52 39 S(=O)(=O)(Nc1ccc(cc1)NC(=O)C)C=C 28.7 40 S(=O)(=O)(Nc1c(cccc1C)C)C=C 181 41 Clc1ccc(cc1)NS(=O)(=O)C=C 22.2 42 N(c1cnc(cc1)OC)C(=O)C#C 14.8 43 S(=O)(=O)(N2Cc1ncccc1C2)C=C 10.5 44 S(=O)(=O)(N1CCC(CC1)Nc2nc(ccn2)-c3n(c(nc3)C)C(C)C)C=C 49.5 45 Fc1c(cccc1Nc2ncnc3c2cc(c(c3)OC)OC4CCN(CC4)S(=O)(=O)C=C)Cl 55.7 46 Clc1c(cc(c(c1)OCC(=O)N2CCC(CC2)NS(=O)(=O)C=C)O)Cl 180 47 Clc1c(cc(c(c1)NCC(=O)N2CCN(CC2)S(=O)(=O)C=C)OC)Cl 17.5 S3
48 Clc1c(cc(c(c1)NCC(=O)N2CCC(CC2)NC(=O)C#C)OC)Cl 77.4 49 Clc1c(cc(c(c1)NCC(=O)N2CCN(CC2)C(=O)C#C)OC)Cl 24.1 50 Clc1c(cc(c(c1)NCC(=O)N2[C@@H]3CN([C@H](C2)C3)S(=O)(=O)C=C)OC)C l 33.3 51 N(c1onc(c1)-c2ccccc2)C(=O)C=C 4.09 52 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 6.16 1 9a c1cc(ccc1n)f 4.64 2 10a c1ccc(cc1)cn 9.40 3 11a CNc1ccccc1 4.85 4 12a c1ccc(cc1)n 4.60 5 13a Cc1ccccc1N 4.57 5 14a COc1ccc(cc1)N 5.25 6 15a c1ccc(c(c1)c#n)n 1.80 7 16a c1cc(cc(c1)f)n 3.59 2 17a Cc1ccc(cc1)N 5.08 6 19a c1cc(ccc1c#n)n 1.74 8 24a 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)cncc2 4.95 Internal 27a CCc1cccc(c1)Nc2c3cc(c(cc3ncc2C(=O)N)OC)NC(=O)[C@@H]4CC CN4 8.25 Internal 28a c1ccc2c(c1)nnn2c3c(ncc(n3)c4cnn(c4)c5ccncc5)n 9.08 Internal 29a c1c(c(cc(c1i)cl)o)ncc(=o)n2ccncc2 7.82 Internal 30a COc1cc(c(cc1NCC(=O)N2CCNCC2)Cl)Cl 7.91 Internal 31a c1ccc(cc1)c2cnc(nc2)n3ccncc3 8.65 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-])nccn2 2.97 Internal 55a CS(=O)(=O)c1ccc(cc1)c2ccc(nc2)N3CCNCC3 8.72 Internal S4
Table S3. GSH t 1/2 and QM data for compounds 56-86 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-] 78-0.094 1.819 Y 57 CC(=O)c1ccc(cc1)NC(=O)CCl 110-0.066 1.820 Y 58 c1cc(cc(c1)f)nc(=o)ccl 153-0.031 1.822 Y 59 c1cc(ccc1nc(=o)ccl)br 164-0.033 1.821 Y 60 Cc1ccc(cc1)NC(=O)CCl 219-0.023 1.823 Y 61 CCOc1ccc(cc1)NC(=O)CCl 235-0.019 1.823 Y 62 Cc1ccccc1NC(=O)CCl 337-0.026 1.825 Y 63 c1ccc(c(c1)c(f)(f)f)nc(=o)ccl 449-0.040 1.822 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 20.9-0.043 1.832 N 75 c1cc(ccc1/c=c/s(=o)(=o)n2ccn(cc 2)C(=O)CCl)Cl 37.1-0.068 1.828 N 76 c1ccc2c(c1)nc(nn2)nc(=o)ccl 41.3-0.106 1.819 Y 77 Cc1csc(c1C#N)NC(=O)CCl 47.2-0.058 1.816 Y 78 c1ccc(cc1)n2ccn(cc2)c(=o)ccl 51.3-0.004 1.805 N 79 CN(Cc1ccccc1)C(=O)CCl 57-0.009 1.806 N 80 C(C(=O)Nc1c(c(nc(c1F)F)F)F)Cl 102-0.060 1.818 Y 81 CN(c1ccccc1)C(=O)CCl 145-0.020 1.804 N 82 Cc1ccc(cc1NC(=O)CCl)C#N 193-0.053 1.824 Y 83 c1ccc(cc1)nc(=o)ccl 199-0.025 1.823 Y 84 COc1ccc(c(c1)NC(=O)CCl)OC 258-0.027 1.822 Y 85 c1ccc(cc1)ccnc(=o)ccl 615-0.005 1.824 Y 86 CC(C)(CNC(=O)CCl)c1ccccc1 667-0.005 1.826 Y C-Cl parallel to N-H? S5
Table S4. QM energies of compounds (E C ), Me-S adducts (E Add ), transition states (E TS ) and LUMO (E LUMO ) for 8-23. 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 8-533.519612-971.684934-971.680349-0.025 9-577.387051-1015.555853-1015.550010-0.029 10-517.471063-955.635186-955.632336-0.017 11-517.455696-955.626958-955.619201-0.026 12-478.176191-916.344682-916.338913-0.029 13-517.475112-955.643819-955.637670-0.029 14-592.659622-1030.826255-1030.821269-0.026 15-570.395715-1008.571451-1008.562628-0.045 16-577.387853-1015.559736-1015.552813-0.032 17-517.474889-955.642318-955.637024-0.028 18-494.219927-932.391978-932.384519-0.035 19-570.398385-1008.573337-1008.564214-0.045 20-635.362570-1073.518253-1073.514498-0.006 21-517.475109-955.638178-955.634141-0.026 22-556.776120-994.935553-994.930844-0.018 23-517.478269-955.642203-955.637399-0.023 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. 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. Figure S4. Lowest unoccupied molecular orbital (LUMO) of 24 S8
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
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
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
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) 20 Compound 12 C 0.68200-0.29730-0.00060 N -0.67370-0.67990-0.00120 C 1.63130-1.32990 0.00070 C 1.11160 1.03620-0.00140 C -1.78730 0.11080 0.00010 C 2.98990-1.03700 0.00120 C 2.47980 1.31240-0.00090 C -3.06890-0.65700-0.00110 O -1.75320 1.33870 0.00190 C 3.42470 0.28950 0.00040 C -4.23690-0.01660 0.00070 H -0.83690-1.67840-0.00210 H 1.29890-2.36470 0.00140 H 0.38810 1.83840-0.00250 H 3.70890-1.85020 0.00220 H 2.80330 2.34890-0.00160 H -3.02080-1.74300-0.00330 H 4.48500 0.51950 0.00080 H -5.17690-0.55710-0.00010 H -4.26600 1.06930 0.00290 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) 25 Compound 12 SMe adduct S 4.23460-0.08380 0.38860 C 3.03090-0.45000-1.02000 C 1.71810-0.98630-0.62070 C 0.59390-0.16810-0.56560 O 0.52150 1.05740-0.88630 N -0.59360-0.81240-0.10050 C -1.89210-0.34610-0.01000 C -2.30310 0.95870-0.35440 C -3.64050 1.32850-0.21800 C -4.60540 0.43880 0.25420 C -4.20290-0.85510 0.59490 C -2.87520-1.24210 0.46650 C 3.20470 1.04180 1.36540 H 2.91550 0.49160-1.56360 H 3.61930-1.13830-1.63530 H 1.65060-2.02090-0.29410 H -0.47120-1.78040 0.16320 H -1.56550 1.65810-0.72030 H -3.92830 2.34070-0.49050 H -5.64210 0.74290 0.35420 H -4.92860-1.57330 0.96630 H -2.58120-2.25330 0.73800 H 3.66370 1.16520 2.34770 H 3.11610 2.01650 0.88070 H 2.21110 0.59880 1.47630 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) 25 Compound 12 SMe transition state S -4.22810-0.49880 0.31870 C -2.95320 0.93560-0.97930 C -1.73300 1.27420-0.39920 C -0.58080 0.44450-0.60280 O -0.56290-0.59700-1.28910 N 0.58060 0.89300 0.03410 C 1.86370 0.34630 0.04100 C 2.20340-0.88410-0.54800 C 3.51790-1.34650-0.47470 C 4.51300-0.61750 0.17380 C 4.17440 0.60370 0.76100 C 2.87100 1.08020 0.69620 C -2.94060-0.95250 1.50960 H -2.92720 0.25530-1.82320 H -3.73340 1.68700-1.01980 H -1.66150 2.11420 0.28620 H 0.48470 1.76310 0.54000 H 1.44160-1.45920-1.05340 H 3.76040-2.29960-0.93620 H 5.53050-0.99080 0.22240 H 4.92940 1.19260 1.27320 H 2.62030 2.03300 1.15590 H -3.28940-0.83310 2.53780 H -2.59870-1.98110 1.36960 H -2.08300-0.27780 1.35650 S15
References 1. Willi, A. V., Die Substituentenwirkung der NH3+-Gruppe auf die Ionisationskonstante einer aromatischen Base. Z. Phys. Chem. 1961, 27, 233-238. 2. 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, 388-393. 3. 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, 461-466. 4. Horrobin, S., The hydrolysis of some chloro-1,3,5-triazines: mechanism: structure and reactivity. J. Chem. Soc. 1963, 4130. 5. Bolton, P. D.; Hall, F. M., Thermodynamic functions of ionization of the Anilinum and Toluidinium Ions. Australian J. Chem. 1967, 20, 1797. 6. 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, 318-322. 7. 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, 726-727. 8. 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, 4226-4230. S16