Ovarian cancer, as a malignant tumor of the ovaries, can occur at any age. The histological types are diverse and mainly epithelial(25). And because ovarian cancer is not easy to be found in the early stage, the treatment effect is relatively poor in the late stage. The recurrence rate after treatment is high, and the mortality rate is also very high. Prexasertib, as a typical CHK1 inhibitor, has been shown that there is a reliable effect in the treatment of ovarian cancer, especially high-grade serous carcinoma(4).But there are some side effects. In addition,Initial cell abatement surgery and platinum-based chemotherapy are effective against this type of cancer, but it is prone to relapse and eventually develops platinum resistance. For these patients with poor prognosis, new treatment strategies are needed,and other CHK1 inhibitors need to be sought for treatment(26).
DNA damage Response (DDR) is the main regulatory mechanism in tumor formation(7). As a serine-threonine protein kinase, CHK1 could regulate the cellular activities. CHK1 is an important component of DRR pathway and a major regulatory molecule of arresting the cell cycle which is DNA damage-dependent (27). CHK1 contribute to DNA damage repair as a strategic molecule,which is an important cause of malignant tumor growth and a hindrance to treatment. The mechanism which CHK1 inhibitors kill cancer cells is to prevent the phosphorylation of CHK1 itself, resulting in the failure of phosphorylation of its substrate and the failure of cells to stay at the G2-M check point in the process of cell cycle. Thus, the collapse occurs, causing the killing of tumor cells(28, 29). Therefore, the search for a suitable CHK1 inhibitor is crucial to the resistance to tumor growth and treatment to tumor. For the past few years,novel clinical CHK1 inhibitors have been developing and they are given in combination with other anticancer drugs to improve the therapeutic effect of tumor are always of great value and meaningful(4, 16).
Over time, the design and development of CHK1 inhibitors has made great progress(19). As Prexasertib is part of a relatively mature CHK1 inhibitor, we take it for granted as the reference drug in our research. The potential of CHK1 inhibitors in tumor therapy is unquestionable. The detailed structural characteristics of CHK1 and the basis for identifying Prexasertib in this study could help improve the structural design of CHK1 inhibitors and could ultimately be used to improve enzymes for cancer treatment.
In this study, a big part of the main content is to select Discovery Studio 4.5’6 modules (LibDock, ADME, TOPKAT, CDOCKER, 3D-QSAR and molecular dynamics simulation) to screen and analyze the biochemical structure properties of novel potential inhibitors. Apart from these, we also studied and investigated the molecular conformation, pharmacological properties, binding affinity, and stability of the selected compounds to provide stronger evidence for their high performance over the reference inhibitor Prexasertib.
Firstly, there were 17799 named product compounds in the ZINC15 database for us to conduct virtual screening. What’s more, all of these named product molecules were purchasable and natural. The LibDock score served as an indicator of evaluating the effect of energy optimization and conformational stability.Therefore,we can draw the conclusion that the higher the LidDock score is, the better energy optimization and comformational stability are. After scoring these compound by using Discovery Studio 4.5’s libdock module, we first selected 3,394 compounds that were considered to have high affinity with CHK1. At the same time, another 105 compounds were selected on account of having a higher scores in the Libdock module than the reference inhibitor Prexasertib (Lib-dock score: 116.085, ranking: 106) among these compounds. To put it another way, in terms of stable conformation and better energy optimization,these 105 compounds were superior to Prexasertib. Finally, the top 20 natural compounds scoring by LibDock module are selected and concentrated for subsequent research.
Secondly, ADME(absorption, distribution, metabolism, excretion) and toxicity properties are two important indicators to evaluate pharmacological properties of drugs, so we used the ADME module and TOPKAT module to predict these two indicators. AS a result, two compounds(ZINC000008214547 and ZINC000072103632) are considered to be ideal lead compounds. Because they have a good level of dissolution in water, which implies that they can be absorbed well in the body and they show non-inhibition to cytochrome P4502D6(CYP2D6) which means they are no hepatotoxicity. In addition, three toxicity indexes, the Ames mutagenicity, rodent carcinogenicity, and developmental toxicity potential of these two compounds are lower than those of other compounds, which also indicate their potential applications in drug development. Moreover, specific groups and atoms can be designed to alter pharmacological properties. Therefore, We can’t categorically assume that the other compounds on the list that are less desirable. Perhaps, with some design, these compounds can also work in unexpected ways and shows their potential value in drug development. In summary, compared with the current research, ZINC000008214547 and ZINC000072103632 are the most valuable high quality drug candidates and most likely to play the role we expect.
Thirdly, CDOCKER module played an important role in the study of chemical bonding and bonding mechanisms in this study. We obtained CDOCKER interaction energy of ZINC000008214547 and ZINC000072103632 after calculating by CDOCKER module. The values were lower than the reference ligand Prexasertib(-45.4587 kcal/mol)apparently. This leads us to the conclusion that these two molecules can better bind with CHK1 with a high affinity in comparison with Prexasertib. Nevertheless, the chemical structure of these two molecules should also be analyzed, which we do with 3D-QSAR module. The two compounds combined with CHK1 had similar type and number of chemical bonds to Prexasertib, so these two compounds could also stably bind to CHK1 through active site Cys145, which possibly help to competitively inhibit the activity of CHK1 and thus playing a role in increasing tumor lethality.
Furthermore, in the same way, feature pharmacophores of these two compounds is analysed by 3D-QSAR. Computation results illustrated 46 feature pharmacophores in ZINC000008214547 and 16 feature pharmacophores in ZINC000072103632.Apart from these, the result also showed us ZINC000008214547 can act as hydrogen bond donor, hydrogen bond acceptor and hydrophobic center and ZINC000072103632 can act as hydrogen acceptor and hydrophobic center. After predicting the pharmacophore of these two molecules by computational methods. The results mean that these 2 molecules probably have a more suitable and valid pharmacophore than Prexasertib. In future research, diverse specific groups could be added to the two compounds to elaborate the design and refinement of the drugs, thus increasing their significance in drug therapy and drug improvement.
Finally, the stability of these two compounds was appraised by performing molecular dynamics simulation module. The data relating to RMSD and potential energy of these ligand-CHK1 complexes were obtained in this step. And the results displayed that the time of the trajectories of complexes to reach equilibrium is about 85 ps. Both RMSD and potential energy of the complexes don’t change over time and stay stable all the time. So that proved that these 2 complexes have the ability of stable existence in the natural environment. Taking all the above results into consideration, they provides the possibility to develop and design drugs, such as modification and purification, to bind ligands and receptors more firmly. It is also worth noting that a similar skeleton in their chemical structures can represent as agonists or inhibitors, and the inverse effect is caused by the addition or removal of different groups or atoms. From what has been discussed above, the natural compounds identified in this study have the advantages of strong pharmacological action, strong binding affinity with CHK1 and good stabilization, which can provide valuable resources for the development of CHK1-related drugs.
At present, the design and development of oncology drugs has always been a topic of interest to scientists around the world, although the road to research and development of oncology drugs is tortuous and difficult. This study about screening of ideal lead compounds is of great significance and is a crucial step in drug design. It lays a firm foundation for future drug designation and development. Through a sequence of advanced technical calculations, We speculate that these two promising molecules probably possess of bright prospects and significant significance in the future treatment of ovarian cancer. In addition, this study provides effective guidance and techniques for screening lead compounds with some potential therapeutic value. This advanced approach could help identify more lead compounds in the future and contribute to drug development.
Although this study has been carefully designed and accurately measured, we admit that there are still some limitations in this study. In fact, it takes thousands of refinements and refinements to bring a drug to market successfully. Therefore, subsequent research can focus directly on refining and improving the lead compounds selected in this study.