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. 2023 Dec 14;66(23):15629-15647.
doi: 10.1021/acs.jmedchem.3c01233. Epub 2023 Nov 15.

Discovery of KB-0742, a Potent, Selective, Orally Bioavailable Small Molecule Inhibitor of CDK9 for MYC-Dependent Cancers

David B Freeman  1   2 , Tamara D Hopkins  1   2 , Peter J Mikochik  1   2 , Joseph P Vacca  1   2 , Hua Gao  1   2 , Adel Naylor-Olsen  3 , Sonali Rudra  4 , Huixu Li  5 , Marius S Pop  1   2 , Rosa A Villagomez  1   2 , Christina Lee  1   2 , Heng Li  1   2 , Minyun Zhou  1   2 , Douglas C Saffran  1   2 , Nathalie Rioux  6 , Tressa R Hood  1   2 , Melinda A L Day  1   2 , Michael R McKeown  1   2 , Charles Y Lin  1   2 , Norbert Bischofberger  1   2 , B Wesley Trotter  1   2
Affiliations

Discovery of KB-0742, a Potent, Selective, Orally Bioavailable Small Molecule Inhibitor of CDK9 for MYC-Dependent Cancers

David B Freeman et al. J Med Chem. .

Abstract

Transcriptional deregulation is a hallmark of many cancers and is exemplified by genomic amplifications of the MYC family of oncogenes, which occur in at least 20% of all solid tumors in adults. Targeting of transcriptional cofactors and the transcriptional cyclin-dependent kinase (CDK9) has emerged as a therapeutic strategy to interdict deregulated transcriptional activity including oncogenic MYC. Here, we report the structural optimization of a small molecule microarray hit, prioritizing maintenance of CDK9 selectivity while improving on-target potency and overall physicochemical and pharmacokinetic (PK) properties. This led to the discovery of the potent, selective, orally bioavailable CDK9 inhibitor 28 (KB-0742). Compound 28 exhibits in vivo antitumor activity in mouse xenograft models and a projected human PK profile anticipated to enable efficacious oral dosing. Notably, 28 is currently being investigated in a phase 1/2 dose escalation and expansion clinical trial in patients with relapsed or refractory solid tumors.

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Conflict of interest statement

The authors declare no competing financial interest.

Figures

Figure 1
Figure 1
(A) Structure of 1 and (B) predicted docking in the CDK9/cyclinT1 ATP-competitive binding site from crystal structure PDB: 3MY1.
Figure 2
Figure 2
Computational model highlighting the associated strain energy of diamino-cyclopentane diastereomers within the ATP-competitive binding site. (a) Overlay of diamino-cyclopentane diastereomers 28, 38, 39, and 40 within the ATP-competitive binding site of CDK9/cyclin T1. (b) Predicted strain energy (kcal/mol) plotted against the IC50 of each diastereomer.
Figure 3
Figure 3
Crystal structure of 28 bound to the complex of CDK9 (cyan) and cyclin T1 (gray) (PDB: 8K5R). The ligand carbon atoms are shown in orange.
Figure 4
Figure 4
Simulated human pharmacokinetic (PK) profile for oral dosing of compound 28 at 5 mg daily with a clearance of 2 mL/min/kg and a volume distribution projection of 6 L/kg, giving a mean projected drug half-life of 35 h. Assumptions include PK linearity, one compartment, and 75% bioavailability.
Figure 5
Figure 5
Compound 28 decreased the levels of MYC (a) and pSER2 (b) in TNBC PDX CTG-1017 subcutaneous tumors. Tumor-bearing Athymic Nude-Foxn1nu mice were collected at 2 and 8 h post-terminal dose of either vehicle or 60 mg/kg 28 p.o. using an intermittent dosing schedule of 3-days on, 4-days off for up to 4 weekly cycles. Tumor lysates were prepared, and levels of MYC (a) and pSER2 (b) were determined using their respective HTRF assays. The plasma concentration of 28 was 846 ng/mL (2.9 μM) and 73 ng/mL (0.25 μM) at 2 and 8 h post-dose, respectively. Data are presented as mean ± SEM, n = 5. *P < 0.05; **P < 0.005; ***P < 0.0005; ****P < 0.0001. hr: hour; HTRF: homogeneous time-resolved fluorescence; LLoQ: lower limit of quantification; ns: not significant.
Figure 6
Figure 6
In vivo tumor growth inhibition for compound 28 in the TNBC model CTG-1017. Athymic Nude-Foxn1nu mice bearing established subcutaneous PDX tumors (mean starting tumor volume of 157 mm3) were treated with vehicle (saline), 28, or SOC chemotherapeutics (cisplatin and gemcitabine). Vehicle and 28 at 60 mg/kg were administered orally using an intermittent dosing schedule of 3-days on, 4-days off for up to 4 weekly cycles (day 30 TGI = 82%, p = 0.0001 vs vehicle). SOC were administered as follows: cisplatin 5 mg/kg i.p. Q7D×3 + gemcitabine 100 mg/kg i.p. Q7D×3. The corresponding mean body weight over time graph can be found in the Supporting Information.
Figure 7
Figure 7
Numbering convention used for pyrazolo[1,5-a]pyrimidine core.
Scheme 1
Scheme 1. Synthesis of Four-Membered-Ring Minimal Pharmacophore Derivatives through Amination of Chloro-pyrazolo[1,5-a]pyrimidine 43
Reagents and conditions: (a) 1H-pyrazol-5-amine, AcOH, reflux; (b) POCl3, pyridine, DMAP, MeCN, reflux; (c) RNH2, K2CO3, MeCN, reflux; (d) HCl, 1,4-dioxane, 0 °C; (e) LiAlH4, THF, 0–80 °C; (f) Ghaffar–Parkins catalyst, H2O, THF, 70 °C.
Scheme 2
Scheme 2. Modular Elaboration of Aminocyclobutane 8
Reagents and conditions: (a) AC2O, pyridine; (b) S-methyl methylaminomethanethioate, 1,4-dioxane, H2O, 65 °C; (c) diphenyl N-cyanocarbonimidate, iPrOH, 70 °C; (d) MeNH2, iPrOH, 70 °C; (e) MeSO2Cl, NaHCO3, DIPEA, CH2Cl2.
Scheme 3
Scheme 3. Synthesis of Five- and Six-Membered-Ring Minimal Pharmacophore Derivatives through Amination of Chloro-pyrazolo[1,5-a]pyrimidine 43
Reagents and conditions: (a) RNH2, K2CO3, MeCN, reflux; (b) HCl, 1,4-dioxane, 0 °C; (c) S-methyl N-methylcarbamothioate, 1,4-dioxane, H2O, 65 °C.
Scheme 4
Scheme 4. Suzuki–Miyaura Coupling Route to 5-Aryl-Substituted Pyrazolo[1,5-a]pyrimidine Analogues
Reagents and conditions: (a) N1-Boc-((1S,3S)-3-aminocyclopentyl), TEA, MeCN, 50 °C; (b) N1-Boc-(1S,3S)-3-aminocyclopentyl), K2CO3, MeCN, reflux; (c) HCl, EtOAc; (d) ArB(OH)2, Pd2(dba)3, XantPhos, K2CO3, 1,4-dioxane, 100 °C; (e) 4 N HCl, 1,4-dioxane; (f) TFA, CH2Cl2 (g) ArB(OH)2, Pd(dppf)Cl2, K2CO3, 1,4-dioxane, H2O; (h) ArB(OH)2, Pd(PPh3)4, K3PO4, DMF.
Scheme 5
Scheme 5. Synthesis of 1,3-Diaminocyclopentane Isomers via Chloro-pyrazolo[1,5-a]pyrimidine 49
Reagents and conditions: (a) 1H-pyrazol-5-amine, AcOH, reflux; (b) POCl3, pyridine, DMAP, MeCN, reflux; (c) K2CO3, MeCN, reflux; (d) HCl, 1,4-dioxane, 0 °C.
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