Introduction to bio-crystallography through the structural study of the kinase dependent of cycline 2 (CDK2) complexed with inhibitors

Author(s)

Walter Filgueira de Azevedo Junior

• Document type: Doctoral Thesis
• Press: São Carlos.
• Institution: Universidade de São Paulo (USP). Instituto de Física de São Carlos (IFSC/BT)
• Defense date: 1997-04-23

Examining board members

Yvonne Primerano Mascarenhas; Hugo Aguirre Armelin; Raghuvir Krishnaswamy Arni; Aldo Felix Craievich; Richard Charles Garratt

• Advisor: Yvonne Primerano Mascarenhas

Abstract

Cell cycle progression is tightly controlled by the activity of ciclin-dependent kinases (CDKs). CDKs are inactive as monomers, and activation requires binding to cyclins, a diverse family of proteins whose levels oscillate during cell cycle, and phosphorilation by CDK-activating kinase (CAK) on a specific threonine residue. CDKs are able to phosphorylate many proteins that are in volvedin cell cycle events, including histones and tumor suppressor proteins like the retinoblastoma gene product pRb. In addition to the positive regulatory role of cyclins and CAK, many negative regulatory proteins (CDK Inhibitors, CIGs) have been discovered, such as p16, p21, and p28. Since deregulation of cyclins and/or alteration or absence ofCKIs have been associated with many cancers, there is strong interest in chemical inhibitors of CDKs that could play an important role in the discovery of new family of antitumor agents. Since ATP is the authentic cofactor of CDK2 it can be considered as a \"pseudo-lead compound\" for discovery of CDK2 inhibitors. However there are two major concerns: adenine containing compounds are common ligants for many enzymes in cells, thus, any adenine derivatives may inhibit many enzymes in the cells: second, any highly charged compounds such as ATP will prevent them from uptake by cells. We report here the x-ray structures of CDK2 in complex with two different inhibitors, deschloro-flavopiridol(DFP) and Roscovitine. The structure of the binary complex CDK2-DFP was solved by molecular replacement and refined to Rfactor = 20.3% and the structure ofCDK2-Roscovitine was refined to Rfactor = 18.0 %. The deschloro-flavopiridol(DFP) is a flavone with a novel structure, compared to that of polyhydroxylated flavones. Previous studies have shown that flavopiridol, a flavonoid, can inhibit growth of breast and lung carcinoma cell lines. The Roscovitine is an adenine derivative and a potent CDK2 inhibitor. The two inhibitors are competitive inhibitors for ATP binding to CDK2 and bind to the ATP binding pocket ofCDK2. The comparison of the three-dimensional structures of CDK2-DFP and CDK2-Roscovitine with the CDK2-ATP shows that the hydrophobic adenine-binding pocket has a surprising ability to accommodate molecular structures that are different from ATP. (AU)