University of Medical Sciences and Technology

Faculty of pharmacy

Insilco study of inhibition of Cyclin-G-associated kinase (GAK)

This proposal is done to fulfill the MSc. Degree In pharmaceutical technology

By

Awadalkreem Ahmed Fadelallah

Supervisor
Talal Ahmed Awad Mohamed
Co-superviser:
1. Dr. Ayat Ahmed Alrasheid
2.

September, 2021
1.1 Introduction
Cyclin G-associated kinase (GAK) is a serine/threonine kinase that in humans is encoded by
the GAK gene. Associates with cyclin G and CDK5. Seems to act as an auxilin homolog that is
involved in the uncoating of clathrin-coated vesicles by Hsc70 in non-neuronal cells.
GAK (cyclin G-associated kinase) is a key regulator of clathrin-coated vesicle trafficking and
plays a central role during development. Additionally, due to the unusually high plasticity of its
catalytic domain, it is a frequent 'off-target' of clinical kinase inhibitors associated with respiratory
side effects of these drugs(1)
GAK targeting is a new approach for novel drugs to cure cancer, hepatitis & Parkinson.
Duo to GAD expression in cancer cells and the important role which it serves it become a
favorable target for anticancer a triggering apoptosis and death for the cell. If we could find a
selective ligand and we reduced the side-effect we might end up with a cure for serval types of
cancer including breast, prostate and many other types of cancer.(2),(3)
Figer:(1)

1.1.1 Objectives

1.1.2 General Objective

The main objective is to find lead compound from the database against GAK.

1.1.3 Specific Objective

 The aim is to decide whether to go through for the wet lab or not.

 To gain better understanding toward the targets.

 2. Literature review

2.1. Cyclin-G-associated kinase

 The kinases play a pivotal role in regulation of signaling pathways. The structure of GAK was
determined by using X-ray diffraction to a resolution of 2.10 A. the GAK has two domains cytolic
proteins. the one of interest is the C-terminal domain. (4)
 Understanding the function of a kinase requires understanding of its structural plasticity and, as a
consequence, the generation of multiple structures in diverse conformations. GAK was originally
identified as an association partner of cyclin G and CDK5 (cyclin-dependent kinase 5). which is
essential for clathrin trafficking, mediating binding of clathrin to the plasma membrane and the
transGolgi network, and regulating receptor signaling by influencing trafficking downstream of
clathrin-coated vesicles. In addition to its role in the cytoplasm, GAK has important functions in the
nucleus. It is required for the maintenance of proper centrosome maturation and progression through
mitosis. GAK plays a central role during development and GAK -mice die early in gestation. Deleting
GAK in adult mice in an inducible knockout mouse model resulted in death of these animals after 3
weeks, demonstrating that GAK is also essential for the viability of adult mice. Tissue-specific
conditional knockout of GAK in the skin, liver or developing brain also resulted in lethal phenotypes
shortly after birth with severe alteration of the affected tissues and a failure of progenitor cells to
differentiate. The kinase activity of GAK plays an essential role in viability and mice expressing only a
kinase-dead form of GAK also die shortly after birth. Death is caused by respiratory dysfunction due
to altered distribution of surfactant protein. This critical role for GAK in the maintenance of
respiratory function is thought to be the cause of the side effects observed with the EGFR (epidermal
growth factor receptor) kinase inhibitor gefitinib, used in the treatment of patients with NSCLC (non-
small-cell lung cancer). Also it have the major role in apoptosis and cell cycle duo to it induction
within few hours of growth factor stimulation. Diseases associated with GAK include Early-Onset Parkinson's
Disease and Cataract 8, Multiple Types..(5)

2.Methodology
3.1Docking
Is computational method for screening large libraries of compounds and rank the result according to
the highest binding affinity to the ligands. It can propose structural hypotheses of how the ligand
inhibit the target. (6)

3.1 .1 Docking software

Molecular Operating Environment (MOE) 2015.10 is a drug discovery software platform that
integrates visualization, modeling and simulations, as well as methodology development, in one
package.(7)
2.1. 2 Computer
Toshiba laptop satellite L830-8367, core i5 ,64-bit Ram 6, processer 1.7 Hz AMD
3.1. 3 Other software
Chem-draw, pymol, chemoffice, swiss-ADMET & Schrodinger.

3.2.1 Targets:
GAK which we obtained it is structure from protein data bank.
3.2.2 ligands:
We will screen compounds from databases virtually.

3.2.3 ADMET Analysis

After screening the compounds, we will calculate and predict the scores of ADMET process using swiss-
ADMET software.

4. Project timeline
NO. Details duration

1 Creation of targets and ligands 7 days

2 Docking 7 days
3 ADMET study 7 days
4 literature survay 14 day
5 Preparation of Homology modeling 1 month
6 Theses writing 21 days
Total 3 months
 5. References
1. Zhang CX, Engqvist‐Goldstein ÅEY, Carreno S, Owen DJ, Smythe E, Drubin DG. Multiple roles
for cyclin G‐associated kinase in clathrin‐mediated sorting events. Traffic. 2005;6(12):1103–13.
2. Sakurai MA, Ozaki Y, Okuzaki D, Naito Y, Sasakura T, Okamoto A, et al. Gefitinib and luteolin
cause growth arrest of human prostate cancer PC-3 cells via inhibition of cyclin G-associated kinase
and induction of miR-630. PLoS One. 2014;9(6):e100124.
3. Alles MC, Gardiner-Garden M, Nott DJ, Wang Y, Foekens JA, Sutherland RL, et al. Meta-analysis
and gene set enrichment relative to er status reveal elevated activity of MYC and E2F in the “basal”
breast cancer subgroup. PLoS One. 2009;4(3):e4710.
4. Chaikuad A, Keates T, Vincke C, Kaufholz M, Zenn M, Zimmermann B, et al. Structure of cyclin
G-associated kinase (GAK) trapped in different conformations using nanobodies. Biochem J.
2014;459(1):59–69.
5. Asquith CRM, Treiber DK, Zuercher WJ. Utilizing comprehensive and mini-kinome panels to
optimize the selectivity of quinoline inhibitors for cyclin G associated kinase (GAK). Bioorg Med
Chem Lett. 2019;29(14):1727–31.
6. Morris GM, Lim-Wilby M. Molecular docking. In: Molecular modeling of proteins. Springer; 2008.
p. 365–82.
7. Vilar S, Cozza G, Moro S. Medicinal chemistry and the molecular operating environment (MOE):
application of QSAR and molecular docking to drug discovery. Curr Top Med Chem.
2008;8(18):1555–72.