Discovery of Proline-Based p300/CBP Inhibitors Using DNA-Encoded Library Technology in Combination with High-Throughput Screening

Abstract

E1A binding protein (p300) and CREB binding protein (CBP) are two highly homologous and multidomain histone acetyltransferases. These two proteins are involved in many cellular processes by acting as coactivators of a large number of transcription factors. Dysregulation of p300/CBP has been found in a variety of cancers and other diseases, and inhibition has been shown to decrease Myc expression. Herein, we report the identification of a series of highly potent, proline-based small-molecule p300/CBP histone acetyltransferase (HAT) inhibitors using DNA-encoded library technology in combination with high-throughput screening. The strategy of reducing ChromlogD and fluorination of metabolic soft spots was explored to improve the pharmacokinetic properties of potent p300 inhibitors. Fluorination of both cyclobutyl and proline rings of 22 led to not only reduced clearance but also improved cMyc cellular potency.

Discovery of CBPD-268 as an Exceptionally Potent and Orally Efficacious CBP/p300 PROTAC Degrader Capable of Achieving Tumor Regression

“…The final compound 6-((trans-4-(5-acetyl-3- (34). The final compound 34 was prepared from methyl trans-4-hydroxycyclohexane-1-carboxylate (59c) using the similar procedure for synthesis of final compound (35) 64 (33 mg, 1.0 equiv) was dissolved in anhydrous DCM (5 mL), and the solution was degassed and charged 3 times with N 2 . DIBAL (25% in toluene, 153 μL, 4.0 equiv) was added dropwise at −78 °C over 1 h, and the reaction mixture was stirred at −78 °C for an additional 2 h. Then the reaction was quenched with aqueous potassium sodium tartrate and warmed to rt.…”

“…Compound 34 was obtained as a light yellow solid; UPLC-MS: 1. 33 (35) 64 (33 mg, 1.0 equiv) was dissolved in anhydrous DCM (5 mL), and the solution was degassed and charged 3 times with N 2 . DIBAL (25% in toluene, 153 μL, 4.0 equiv) was added dropwise at −78 °C over 1 h, and the reaction mixture was stirred at −78 °C for an additional 2 h. Then the reaction was quenched with aqueous potassium sodium tartrate and warmed to rt.…”

“…CBP/p300 are large proteins and consist of multiple functional domains. In addition to their bromodomain, CBP/p300 contain a histone acetyltransferase (HAT) domain, a plant homeodomain (PHD) finger domain, the nuclear receptor interaction domain (RID), the KIX domain (where CREB and MYB interact), the cysteine/histidine regions (TAZ1/CH1 and TAZ2/CH3), and the interferon response binding domain (IBiD). , Extensive efforts have been made toward discovery of potent CBP/p300 inhibitors in the past decade, ,,− such as bromodomain inhibitors CBP30, I-CBP112, GNE-049 and its analogue GNE-781, , CCS1477 and Y08284, and HAT domain inhibitors C646, A-485, , B026, DS-9300, and CPI-1612, (as shown in Figure ). Interestingly, combination of a bromodomain inhibitor and a HAT domain inhibitor was synergistic in inhibition of prostate cancer cell growth .…”

“…The desired product was eluted when MeCN/H 2 O = 34%. The final compound 6-((trans-4-((5acetyl-3-(7-(difluoromethyl)-6-(1-methyl-1H-pyrazol-4-yl)-3,4-dihydroquinolin-1(2H)-yl)-4,5,6,7-tetrahydro-1H-pyrazolo[4,3-c]pyridin-1-yl)methyl)cyclohexyl)methyl)-2-(2,6-dioxopiperidin-3-yl)-6,7dihydropyrrolo[3,4-f ]isoindole-1,3(2H,5H)-dione(35) was obtained as a white solid (9 mg, 75% yield); UPLC-MS: 1 39. min, purity >99.0%; MS (ESI) m/z calcd for C 45 H 49 F 2 N 9 O 5 [M+H] + 834.4, found 834.40; 1 H NMR (400 MHz, Methanol-d 4 ) δ 7.93 (s, 2H), 7.64 (s, 1H), 7.50 (s, 1H), 7.11 (d, J = 8.6 Hz, 1H), 6.77−6.42 (m, 2H), 5.17(dd, J = 12.5, 5.4 Hz, 1H), 4.94 (s, 4H), 4.27 (d, J = 7.4 Hz, 2H), 3.97−3.86 (m, 6H), 3.82 (t, J = 5.7 Hz, 1H), 3.66 (q, J = 6.8 Hz, 2H), 3.38 (d, J = 6.7 Hz, 2H), 2.96−2.67 (m, 7H), 2.22−2.06 (m, 5H), 2.00−1.85 (m, 4H), 1.84−1.72 (m, 2H), 1.33−1.12 (m, 5H).…”

Discovery of Novel PROTAC Degraders of p300/CBP as Potential Therapeutics for Hepatocellular Carcinoma

“…Multiple domains have been characterized in p300/CBP protein. ,, Among them, the histone acetyltransferase (HAT) domain catalyzes the acetylation of lysine residues on histone tails, directly altering chromatin architecture and thereby promoting transcriptional activation of target genes. , The acetyl-lysine (Kac) binding function of bromodomain (BD) mediates the recognition and engagement of p300/CBP to the enhancer and promotor of target genes and is essential for HAT activity. , Due to the critical role of p300/CBP HAT domain and bromodomain in oncogenic transcription, enormous medicinal efforts have been made, , and our group also previously reported several series of potent and selective small-molecule inhibitors targeting these domains. − Although a few potent and drug-like HAT inhibitors have been reported, − none of them have yet entered clinical development. Notably, a recent study revealed that the elevated intracellular AcCoA, the substrate of the HAT domain, confers acquired resistance to current HAT inhibitors in cancer cells .…”