CDK9

Detailed Information

CDK9 (Cyclin-Dependent Kinase 9) is an important member of the cyclin-dependent kinase family. Highly similar to the gene products of yeast cdc28 and cdc2, CDK9 is part of this family and is thus essential for transcription control, cell cycle progression, and the pathogenesis of many illnesses. Recent research indicates that CDK9 is involved significantly in many pathogenic processes, including viral infections, inflammatory responses, cardiovascular disorders, and the growth of certain tumors. Because of this, CDK9 is becoming more and more appealing as a therapeutic target for drug research; meanwhile, great advancement has been achieved in the creation of its inhibitors.

Molecular Characteristics and Structural Function

Originally called PITALRE, CDK9 got its name from its distinctive amino acid motif (Pro-Ile-Thr-Ala-Leu-Arg-Glu). Two main isoforms—CDK942 and CDK955—are encoded by the CDK9 gene in human cells. Structurally, these isoforms vary; CDK955 has an extra 117 amino acids at the N-terminus than CDK942. They show clear variations in cellular distribution and expression patterns even if their phosphorylation patterns are comparable. While CDK955 is mostly found in the nucleolus and is highly expressed in the liver, brain, and lungs, studies have shown that CDK942 is mostly found in the nucleoplasm and is strongly expressed in tissues including the testes and spleen. These isoforms also show varied expression characteristics throughout cell development. For instance, although CDK955 expression is particularly enhanced during monocyte-to-macrophage development, CDK942 is mostly expressed in undifferentiated monocytes. Cell types and cellular signaling pathways are intimately linked in controlling this varying expression pattern.

Figure 1. CDK9-containing elongation complexes and their functional interplay. (Bacon CW, et al., 2019)

Biological Functions and Molecular Mechanism

The core function of CDK9 is to participate in regulating transcription elongation. In cells, CDK9 achieves its biological functions by forming functional complexes with different regulatory proteins. This process involves multiple important steps and regulatory mechanisms. Firstly, due to the intrinsic instability of the CDK9 monomer, it needs to form transient complexes with several chaperone proteins, including CDC37, HSP70, and HSP90, which are crucial for maintaining CDK9's stability and function. Subsequently, CDK9 is released from this transient complex and binds with cyclins (including T1, T2, and K) to form the P-TEFb complex. During this process, a critical phosphorylation modification occurs at the Thr186 residue on the T-loop of CDK9, which is decisive for activating the P-TEFb complex.

The activated P-TEFb complex can specifically recognize and phosphorylate the Ser2 residues within the C-terminal domain (CTD) of RNA polymerase II. This phosphorylation is a crucial step in initiating and maintaining the transcription elongation process. In addition to its role in transcription elongation regulation, CDK9 is involved in multiple important cellular biological processes such as chromosomal modification, mRNA processing, and nuclear export. This multifunctionality makes CDK9 a vital molecular switch connecting cell cycle regulation and gene expression.

Participating in the control of transcription elongation is CDK9's main job. CDK9 performs its biological role in cells by creating functional complexes between many regulating proteins. There are many significant phases to this process and several regulating systems. First, the CDK9 monomer's inherent instability requires it to form temporary complexes with multiple chaperone proteins, including CDC37, HSP70, and HSP90, which are very vital for preserving CDK9's stability and function. After that, CDK9 comes out of this transitory complex and hooks with cyclins (including T1, T2, and K) to create the P-TEFb complexes. Crucially for activating the P-TEFb complex, a phosphorylation change takes place at the Thr186 residue on the T-loop of CDK9 during this process.

Within the C-terminal domain (CTD) of RNA polymerase II, the active P-TEFb complex may especially identify and phosphorylate the Ser2 residues. Starting and maintaining the elongation of transcription depends critically on this phosphorylation. Apart from its function in transcription elongation control, CDK9 is engaged in other crucial cellular biological events including nuclear export, mRNA processing, and chromosomal alteration. CDK9's multifarious nature makes it an essential molecular switch linking gene expression to cell cycle control.

Viral Infections and Inflammatory Responses

Highly investigated in the framework of HIV infection, CDK9 has a specific function in viral diseases. Studies on the HIV-1 trans-activator protein (TAT) have shown that it may interact especially with CDK9 and its regulating constituent cyclin T1. Viral gene transcription and replication depend on this connection, which emphasizes CDK9's fundamental part in the pathogenesis of AIDS.

CDK9 controls the production of the anti-apoptotic protein Mcl-1, therefore influencing the fate of neutrophils during inflammatory reactions. Key events in the resolution of inflammation are the neutrophils' death and their removal by macrophages. Dysregulation of this mechanism could cause persistent inflammation. Studies show that blocking CDK9 activity may lower Mcl-1 expression levels, encourage neutrophil death, and provide new treatment ideas for inflammatory illnesses.

Cardiovascular Diseases

Particularly in the development of severe ventricular hypertrophy, the function of CDK9 is becoming increasingly appreciated in cardiovascular disorders. Common adaptive change in the heart, pathological cardiac hypertrophy is mainly the consequence of unbalanced growth between myocardial cells and coronary arteries. Studies show that the hypertrophy of cardiac cells is intimately linked to higher protein synthesis motivated by higher general RNA levels in cells. Under this mechanism, CDK9 directly helps to control this pathogenic process by adjusting RNA polymerase II activity; RNA polymerase II, in charge of encoding RNA transcription, is regarded as a limiting factor.

Hematologic Malignancies

Especially in acute myeloid leukemia (AML), the function of CDK9 has been extensively studied in hematologic malignancies. Studies have shown that variations in AML subtypes greatly raised levels of CDK9 mRNA expression in samples of AML patients. Through control of numerous important anti-apoptotic proteins including Mcl-1, Bcl-2, XIAP, and Myc, CDK9 mostly affects leukemia cell survival. Among them, Myc is often overexpressed in many hematologic and solid malignancies, controlling processes including cell proliferation, cell cycle progression, differentiation, and death. Especially in drug-resistant AML, abnormal activation of the CDK9-Myc signaling pathway is intimately linked to disease progression and prognosis.

Furthermore, studies show that via changing the activity of MLL fusion genes, CDK9 contributes to disease progression in mixed-lineage leukemia (MLL). Through influencing transcription elongation processes, the MLL gene may create fusion genes combining many partner genes (such as ENL, AF4, AF9, and AF10), therefore boosting leukemia incidence.

Hepatocellular Carcinoma

Research on hepatocellular carcinoma (HCC) also finds that CDK9 is quite important. HCC's pathogenesis has been a research focus because it ranks fourth among cancer deaths globally. Research indicates that maintaining high expression of the oncogene Myc is intimately correlated with CDK9-mediated transcription elongation. In mice liver cancer models, reducing Myc expression may cause tumor regression; in HCC cells, aberrant expression of Myc can generate aberrant cell proliferation. While the exact processes of Myc's involvement in DNA replication, transcription activation, and elongation are still unknown, sustaining high Myc expression depends on CDK9-mediated transcription elongation.

Prostate Cancer

As prostate cancer (PCa) progresses, CDK9 shows a different kind of activity. Among the most often occurring malignant tumors in males, PCa usually develops from androgen dependency to castration resistance. This mechanism mostly relies on the androgen receptor (AR)-mediated signaling pathway. By phosphorylating the Ser81 residue in the AR domain, research has shown that CDK9 may control AR activity. Particularly in the development towards castration-resistant prostate cancer (CRPC), CDK9 is implicated not only in controlling AR signaling pathways but also in preserving tumor cell life by affecting the production of anti-apoptotic proteins including Bcl-2 and Mcl-1.

CDK9 Inhibitor Research

Since CDK9 plays a major part in many disorders, creating specific CDK9 inhibitors has been a major focus of pharmacological development. Flavonoids, pyrimidines, pyrazoles, pyridines, triazines, and purines are only a few of the various classes into which current CDK9 inhibitors created based on chemical structural features fit. By many modes of action, these inhibitors bring CDK9 activity under control.

Most CDK9 inhibitors bond at the molecular level by means of particular interactions with residues in the CDK9 hinge region. In the hinge region, inhibitor molecules often create distinctive hydrogen bond networks with amino acids using both fork-like hydrogen bonds with carbonyl oxygen atoms and amine hydrogen atoms during the binding process. Nevertheless, conventional ATP-competitive CDK inhibitors usually show poor selectivity as the ATP binding pocket across members of the CDK family has great homogeneity. This lack of selectivity is a major obstacle for the development of present CDK9 inhibitors as it can have several negative effects in clinical settings.