Cyclin-dependent kinase-9 (CDK9) is a serine/threonine protein kinase that plays an important role in cell transcription. Its activation can phosphorylate the C-terminal domain of RNA polymerase II and some transcription factors, and then promote transcription elongation.

Figure 1. Protein structure of CDK9.

CDK9 inhibitor

CDKs were originally discovered as a key component of cell cycle regulation. Because small molecule CDK inhibitors have anti-cell proliferative effects, they are considered compounds with potential for cancer treatment, but recent studies have found that CDK inhibitors also Other effects. Due to the increased expression and activity of CDK9 in cardiac hypertrophy, some scholars have proposed that CDK9 inhibitors can be used as a method for treating cardiac hypertrophy. To date, 30 CDK9 inhibitors have been discovered.

Alvocidib

Alvocidib is a flavonoid alkaloid CDK9 kinase inhibitor under clinical development by Tolero Pharmaceuticals, Inc., which has been studied in clinical development. Its use in treating arthritis and atherosclerotic plaque formation has also been studied. Positive transcription elongation factor P-TEFb. Flavone piperidol treatment of cells can lead to P-TEFb inhibition and reduced mRNA production.

Figure 2. Chemical structure of Alvocidib.

Roscovitine

Roscovitine is a pan-specific CDK inhibitor that significantly inhibits the production of messenger RNA, especially CDK7 and CDK9, which are phosphorylated at the C-terminal domain of RNAPII, and are very sensitive to roscovitine. Roscovitine is the only CDK inhibitor tested in a cardiac mast cell model. Roscovitine can significantly inhibit the hypertrophic growth of cardiomyocytes caused by angiotensin II treatment, and can also effectively inhibit protein synthesis, E2F-dependent transcription, DNA synthesis, and nuclear replication. Roscovitine's anti-hypertrophic activity did not inhibit CDK2 because the expression of non-functional CDK2 mutants did not affect hypertrophic cells. The molecular mechanism of roscovitine's action has not been fully explained.

Figure 3. Chemical structure of Roscovitine.

CDK9 interaction with inhibitor

Most small molecule inhibitors of CDKs are ATP-competitive and bind between the gaps between the two domains. Most inhibitors are hydrophobically bound, but inhibitors that bind to CDK2 also accept a hydrogen bond on the nitrogen of the Leu83 backbone and contribute another hydrogen bond to the carbonyl backbone of Glu81. Some inhibitors also bind to the backbone of the third hydrogen bond of the carbonyl group in Leu83. In addition to binding to the three amino acids threonine, serine, and valine, the inhibitor also interacts with the ribosyl phosphate binding site of CDKs. After the structure of CDK9 has been solved experimentally, the structural model of CDK9 has been used to study the interaction between CDK9 and flavopiridol or CAN508 (flavopiridol and CAN508 are mature and effective inhibitors of CDK9, respectively).

CDK9 and cardiac hypertrophy

Myocardial hypertrophy is a basic response of myocardial cells to hypertension, valvular disease, acute myocardial infarction, and congenital heart disease. It is an independent risk factor that affects the mortality and incidence of cardiovascular disease. Pathological myocardial hypertrophy is the result of an imbalance in the growth of cardiomyocytes and coronary arteries. Cardiac transcription factors directly regulate gene expression of cardiac muscle cells induced by hypertrophic stimulation and play an important role in cardiac hypertrophy. Cardiac cell hypertrophy can be attributed to increased protein synthesis caused by an increase in the overall intracellular RNA content, and RNA polymerase Ⅱ (RNA polymerase II, RNAPⅡ), which is responsible for encoding the transcription of RNA, is considered to be a limiting factor for cardiac hypertrophy, especially In the highly polymerized heptapeptide motif, the phosphorylated serine 2C-terminal domain expresses fully elongated RNAP II and is closely related to cardiac hypertrophy. The prototype kinase that catalyzes the phosphorylation of serine 2 is positive transcription elongation factor B (P-TEFb). In addition to phosphorylated serine 2, P-TEFb also triggers transcription elongation by overcoming the inhibitory effect of negative elongation factor long. P-TEFb usually binds to heat shock protein 70, JunB, mitogen-activated protein kinase phosphatase genes, or other proximal promoter regions that transcribe RNAs. Active P-TEFb is composed of CDK9 and cyclin T1, T2a or T2b, while 7SK small nuclear RNNA (7SK snRNA), six methylene bisacetamide inducible protein 1, Hexim1, 7SK snRNA Methyl phosphate and La-related protein 7 form a "big" complex capping enzyme, inhibiting P-TEFb activity.

Reference:

1. MacLachlan TK; et al. Binding of CDK9 to TRAF2. J. Cell. Biochem. 1998, 71 (4): 467–78.