Late-Stage Functionalization for the Optimization of Reversible BTK Inhibitors

Abstract

Late-stage functionalization (LSF) enables medicinal chemists to quickly explore structure–activity relationships (SAR) of novel analogues derived from a fully elaborated parent structure. Using several known C–H functionalization chemistries, we have systematically applied the LSF strategy to modify different regions of a Bruton’s tyrosine kinase (BTK) reversible inhibitor lead series. This approach allowed for broad SAR exploration across several key subunits of the molecule at positions that were previously difficult to explore with traditional synthesis, providing analogues with high potency and improved pharmacokinetic properties. This case study illustrates both the promise and the challenges associated with applying LSF to complex lead molecules.

Key words

LSF - C–H activation - BTK

Publication History

Received: 13 March 2022

Accepted after revision: 23 April 2022

Article published online:
20 May 2022

• References and Notes

• 1 Steinmetz KL, Spack EG. In The Basics of Preclinical Drug Development for Neurodegenerative Disease Indications, BMC Neurology, 2009. Springer; Berlin: 2009: S2
• 2 Boström J, Brown DG, Young RJ, Keserü GM. Nat. Rev. Drug Discovery 2018; 17: 709
• 3 Hartwig JF. J. Am. Chem. Soc. 2016; 138: 2
• 4 Börgel J, Ritter T. Chem 2020; 6: 1877
• 5a Dombrowski AW, Gesmundo NJ, Aguirre AL, Sarris KA, Young JM, Bogdan AR, Martin MC, Gedeon S, Wang Y. ACS Med. Chem. Lett. 2020; 11: 597
• 5b Guillemard L, Kaplaneris N, Ackermann L, Johansson M. J. Nat. Rev. Chem. 2021; 5: 522
• 5c Moir M, Danon JJ, Reekie TA, Kassiou M. Expert Opin. Drug Discovery 2019; 14: 1137
• 6 Cernak T, Dykstra KD, Tyagarajan S, Vachal P, Krska SW. Chem. Soc. Rev. 2016; 45: 546
• 7a Cunningham-Rundles C, Ponda PP. Nat. Rev. Immunol. 2005; 5: 880
• 7b Kurosaki T, Hikida M. Immunol. Rev. 2009; 228: 132
• 7c Tsukada S, Saffran DC, Rawlings DJ, Parolini O, Allen RC, Klisak I, Sparkes RS, Kubagawa H, Mohandas T, Quan S. Cell 1993; 72: 279
• 7d Vetrie D, Vořechovský I, Sideras P, Holland J, Davies A, Flinter F, Hammarström L, Kinnon C, Levinsky R, Bobrow M. Nature 1993; 361: 226
• 8 Charalambous A, Schwarzbich M.-A, Witzens-Harig M. Ibrutinib. In Small Molecules in Hematology. Springer; Berlin: 2018: 133
• 9 Kriegsmann K, Kriegsmann M, Witzens-Harig M. Acalabrutinib, a Second-Generation Bruton’s Tyrosine Kinase Inhibitor. In Small Molecules in Hematology. Springer; Berlin: 2018: 285
• 10 Syed YY. Drugs 2020; 80: 91
• 11a Boga SB, Alhassan A.-B, Liu J, Guiadeen D, Krikorian A, Gao X, Wang J, Yu Y, Anand R, Liu S, Yang C, Wu H, Cai J, Zhu H, Desai J, Maloney K, Gao Y.-D, Fischmann TO, Presland J, Mansueto M, Xu Z, Leccese E, Knemeyer I, Garlisi CG, Bays N, Stivers P, Brandish PE, Hicks A, Cooper A, Kim RM, Kozlowski JA. Bioorg. Med. Chem. Lett. 2017; 27: 3939
• 11b Gao X, Wang J, Liu J, Guiadeen D, Krikorian A, Boga SB, Alhassan A.-B, Selyutin O, Yu W, Yu Y. Bioorg. Med. Chem. Lett. 2017; 27: 1471
• 12 Liu J, Guiadeen D, Krikorian A, Gao X, Wang J, Babu Boga S, Alhassan A.-B, Yu W, Selyutin O, Yu Y, Anand R, Xu J, Kelly J, Duffy JL, Liu S, Yang C, Wu H, Cai J, Bennett C, Maloney KM, Tyagarajan S, Gao Y.-D, Fischmann TO, Presland J, Mansueto M, Xu Z, Leccese E, Zhang-Hoover J, Knemeyer I, Garlisi CG, Stivers P, Brandish PE, Hicks A, Kim R, Kozlowski JA. Bioorg. Med. Chem. Lett. 2020; 30: 127390
• 13 Liu J, Guiadeen D, Krikorian A, Gao X, Wang J, Boga SB, Alhassan A.-B, Yu Y, Vaccaro H, Liu S, Yang C, Wu H, Cooper A, de Man J, Kaptein A, Maloney K, Hornak V, Gao Y.-D, Fischmann TO, Raaijmakers H, Vu-Pham D, Presland J, Mansueto M, Xu Z, Leccese E, Zhang-Hoover J, Knemeyer I, Garlisi CG, Bays N, Stivers P, Brandish PE, Hicks A, Kim R, Kozlowski JA. ACS Med. Chem. Lett. 2016; 7: 198
• 14a Duncton MA. MedChemComm 2011; 2: 1135
• 14b Proctor RS, Phipps RJ. Angew. Chem. Int. Ed. 2019; 58: 13666
• 15a Matsui JK, Primer DN, Molander GA. Chem. Sci. 2017; 8: 3512
• 15b Molander GA, Colombel V, Braz VA. Org. Lett. 2011; 13: 1852
• 15c Presset M, Fleury-Brégeot N, Oehlrich D, Rombouts F, Molander GA. J. Org. Chem. 2013; 78: 4615
• 16 DiRocco DA, Dykstra K, Krska S, Vachal P, Conway DV, Tudge M. Angew. Chem. Int. Ed. 2014; 53: 4802
• 17a Hartwig JF. Chem. Soc. Rev. 2011; 40: 1992
• 17b Ros A, Fernández R, Lassaletta JM. Chem. Soc. Rev. 2014; 43: 3229
• 18 Hartwig JF. Acc. Chem. Res. 2012; 45: 864
• 19a Wright JS, Scott PJ, Steel PG. Angew. Chem. 2020; 6: 2796
• 19b Preshlock SM, Ghaffari B, Maligres PE, Krska SW, Maleczka RE. Jr, Smith MR. III. J. Am. Chem. Soc. 2013; 135: 7572
• 19c Larsen MA, Hartwig JF. J. Am. Chem. Soc. 2014; 136: 4287
• 20 Wu H, Hynes JJr. Org. Lett. 2010; 12: 1192
• 21a Bissonnette NB, Boyd MJ, May GD, Giroux S, Nuhant PJ. Org. Chem. 2018; 83: 10933
• 21b Yao T, Hirano K, Satoh T, Miura M. Chem. Eur. J. 2010; 16: 12307
• 22 Kim R, Liu J, Gao X, Boga S, Guiadeen D, Kozlowski J, Yu W, Anand R, Yu Y, Selyutin O. US20140206681A1, 2014
• 23 These compounds were found to be stable under the conditions identified for 5; i.e., no decomposition was observed, only recovered starting material. Based on this observation, we speculate that the introduction of the A and B rings into the fully elaborated structures somehow electronically stabilizes these dearomatized adducts and thus hinders their rearomatization.
• 24 Procedure for the Synthesis of 4-{8-Amino-3-[(6R,8aS)-3-oxooctahydroindolizin-6-yl]imidazo[1,5-a]pyrazin-1-yl}-N-[6-isopropyl-4-(trifluoromethyl)pyridin-2-yl]benzamide (2a) Potassium isopropyltrifluoroborate (16.81 mg, 0.112mmol) and benzamide 1 (30 mg, 0.056 mmol) were dissolved in a 1:1 mixture of acetic acid/water (0.8 mL) and TFA (4.32 μL, 0.056 mmol). The resulting mixture was stirred at room temperature until complete dissolution. Then manganese(III) acetate dihydrate (37.5 mg, 0.140 mmol) was added in one portion. The reaction mixture was stirred at 50 °C for 18 h. After cooling to room temperature, the mixture was slowly added to a saturated aq. solution of Na₂CO₃ (5 mL). The aqueous layer then was extracted with EtOAc (3 × 10 mL). The combined organic layers were washed with water (2 × 10 mL), then dried using magnesium sulfate, filtered, and evaporated under vacuum. The residue was purified by preparative reverse-phase HPLC (Waters CSH C18 OBD Prep Column, 19 mm × 150 mm, 5 mm particle size 5 mm, flow = 25 mL/min, gradient: starting with 35% MeCN/water to 80% MeCN/water buffered with 0.16% TFA), to give the the product as a yellowish cream color solid after lyophilization (8 mg, 25% yield). ¹H NMR (499 MHz, CD₃OD): δ = 8.47 (s, 1 H), 8.19–8.15 (m, 2 H), 7.86–7.82 (m, 2 H), 7.68 (d, J = 5.2 Hz, 1 H), 7.32 (s, 1 H), 7.11 (d, J = 5.2 Hz, 1 H), 4.32 (ddd, J = 12.8, 4.4, 1.8 Hz, 1 H), 3.75–3.69 (m, 1 H), 3.35–3.27 (m, 1 H), 3.21–3.13 (m, 2 H), 2.50–2.47 (m, 2 H), 2.42–2.30 (m, 1 H), 2.23 (d, J = 13.9 Hz, 1 H), 2.17–1.96 (m, 2 H), 1.79–1.73 (m, 1 H), 1.55 (qd, J = 13.0, 3.4 Hz, 1 H), 1.40–1.33 (m, 6 H). LCMS (ESI): m/z calcd for [(C₃₀H₃₀F₃N₇O₂) + H]⁺: 578.25; found: 578.43. Procedure for the Synthesis of 4-{8-Amino-3-[(6R,8aS)-3-oxooctahydroindolizin-6-yl]imidazo[1,5-a]pyrazin-1-yl}-N-[6-cyclobutyl-4-(trifluoromethyl)pyridin-2-yl]benzamide (2b) Synthesized as outlined for compound 2a except using potassium cyclobutyltrifluoroborate (15 mg, 0.093 mmol) as the radical source. Product obtained as a white solid (6 mg, 22% yield). ¹H NMR (499 MHz, CD₃OD): δ = 8.46 (s, 1 H), 8.20–8.14 (m, 2 H), 7.86–7.82 (m, 2 H), 7.68 (d, J = 5.2 Hz, 1 H), 7.28 (s, 1 H), 7.11 (d, J = 5.1 Hz, 1 H), 4.32 (ddd, J = 12.9, 4.4, 1.8 Hz, 1 H), 3.84–3.65 (m, 2 H), 3.34–3.27 (m, 1 H), 3.19 (t, J = 12.3 Hz, 1 H), 2.52–2.31 (m, 7 H), 2.25–2.20 (m, 1 H), 2.18–1.90 (m, 4 H), 1.76 (m, 1 H), 1.55 (qd, J = 13.0, 3.4 Hz, 1 H). LCMS (ESI): m/z calcd for [(C₃₁H₃₀F₃N₇O₂) + H]⁺: 590.25; found: 590.4. Procedure for the Synthesis of 4-{8-Amino-3-[(6R,8aS)-3-oxooctahydroindolizin-6-yl]imidazo[1,5-a]pyrazin-1-yl}-N-[6-methyl-4-(trifluoromethyl)pyridin-2-yl]benzamide (2c) and 4-{8-Amino-3-[(6R,8aS)-3-oxooctahydroindolizin-6-yl]imidazo[1,5-a]pyrazin-1-yl}-N-[3-methyl-4-(trifluoromethyl)pyridin-2-yl]benzamide (2d) A solution of benzamide 1 (50 mg, 0.093 mmol), tris(4,7-diphenyl-1,10-phenanthroline)ruthenium(II) dichloride complex (1.09 mg, 93 μmol), and tert-butylperacetate (123 mg, 0.46 mmol) in 0.93 mL MeCN/0.09 mL TFA was degassed by bubbling nitrogen through it for 5 min and then irradiated with a 30 W blue LED lamp for 16 h. The reaction mixture was filtered through a 0.25 micron frit, diluted with DMSO, and purified using preparative reverse-phase HPLC (Waters Xbridge C-18, 30 × 250 mm Prep Column, 30 mm × 250 mm, 5 mm particle size, flow = 50 mL/min, gradient: starting with 20% MeCN/water to 100% MeCN/water buffered with 0.16% NH₄OH), to give the two products 2c and 2d. Prior to evaporation, the two products were analyzed (Waters BEH C-18 column, 2.1 mm × 50 mm, 1.7 μm particle size, flow = 1 mL/min, gradient: starting with 0% MeCN/water to 100% MeCN/water buffered with 0.16% NH₄OH in 1.4 min) to provide the retention times as shown below. Lyophilization provided the products 2c and 2d as white solids. Compound 2c: t_R = 0.84 min; major product (8 mg, 26%). ¹H NMR (600 MHz, CDCl₃): δ = 8.71 (s, 1 H), 8.52 (s, 1 H), 8.11–8.04 (m, 2 H), 7.87–7.83 (m, 2 H), 7.33 (d, J = 5.1 Hz, 1 H), 7.18 (s, 1 H), 7.16 (d, J = 5.0 Hz, 1 H), 4.45 (ddd, J = 12.8, 4.2, 1.8 Hz, 1 H), 3.65–3.59 (m, 1 H), 3.16–3.03 (m, 2 H), 2.58 (s, 3 H), 2.50–2.46 (m, 2 H), 2.37–2.29 (m, 1 H), 2.28–2.08 (m, 3 H), 1.77–1.67 (m, 1 H), 1.44 (tdd, J = 13.1, 11.4, 3.8 Hz, 1 H), 4.45 (ddd, J = 12.8, 4.2, 1.8 Hz, 1 H), 3.65–3.59 (m, 1 H), 3.16–3.03 (m, 2 H), 2.58 (s, 3 H), 2.50–2.46 (m, 2 H), 2.37–2.29 (m, 1 H), 2.28–2.08 (m, 3 H), 1.77–1.67 (m, 1 H), 1.44 (tdd, J = 13.1, 11.4, 3.8 Hz, 1 H). LCMS (ESI): m/z calcd for [(C₂₈H₂₆F₃N₇O₂) + H]⁺: 550.22; found: 550.2. Compound 2d: t_R = 0.76 min; minor product (2 mg, 6.5%). ¹H NMR (600 MHz, CDCl₃): δ = 8.46 (d, J = 5.1 Hz, 1 H), 8.41 (s, 1 H), 8.09 (d, J = 7.9 Hz, 2 H), 7.83 (d, J = 8.1 Hz, 2 H), 7.49 (d, J = 5.0 Hz, 1 H), 7.32 (d, J = 5.1 Hz, 1 H), 7.13 (d, J = 5.1 Hz, 1 H), 5.54 (br s, 2 H), 4.44 (ddd, J = 12.8, 4.3, 1.8 Hz, 1 H), 3.65–3.60 (m, 1 H), 3.16–3.01 (m, 2 H), 2.52–2.38 (m, 5 H), 2.36–2.28 (m, 1 H), 2.28–2.06 (m, 3 H), 1.75–1.69 (m, 1 H), 1.49–1.37 (m, 1 H). LCMS (ESI): m/z calcd for [(C₂₈H₂₆F₃N₇O₂) + H]⁺: 550.22; found: 550.2