CDK2 Enzyme Research Articles

Synthesis, anticancer activity, docking and computational studies of new pyridyl-glycosyl hybrids and acyclic analogs.

New pyridine-O-glycosides and their acyclic nucleoside analogues were prepared by heterocyclization and glycosylation. The anticancer activity against HCT-116, HepG2 and MCF-7 human cancer cells and BJ-1 cell revealed that the galacto- and xylopyranosyl glycosides possessing 4-bromophenyl have superior cytotoxic activities against HepG2 cell while glycosides 7-9 resulted in superior cytotoxic activities regarding MCF-7 breast cell. In case of HCT-116 colorectal carcinoma cells, two products and the derived glycosides and acyclic analogues showed potent activities. The most potent compounds were investigated for their possible binding affinities to the active site of CDK2 enzyme via in silico molecular docking simulation in addition to computational studies. The results support the antiproliferative effect and elucidate the interactions of 3a and 8 with catalytic sites.

Design, synthesis, and molecular docking of novel 1,3, 4-triaryl pyrazole derivatives bearing methylsulfonyl moiety with anticancer activity through dual targeting CDK2 and COX-2 enzymes

Novel 3-(4-methylsulfonylphenyl) pyrazole derivatives with different substitutions at position four were designed, synthesized, characterized by spectroscopic techniques, and investigated as potential anticancer agents via inhibition of cyclin-dependent kinase 2 and cyclooxygenase-2 enzymes. All the synthesized compounds were screened against three cancer cell line panels, hepatocellular carcinoma (HepG-2), mammary gland breast cancer (MCF-7), and colorectal carcinoma (HCT-116), to determine their antiproliferative properties by MTT assay. Compounds 5a, 6a, 6c, and 10c exhibited a considerable antiproliferative effect on HepG-2 cell line with IC50 value of 2.88 to 8.57 µM, on HCT-116 cell line with IC50 value of 6.34 to 17.84 µM, and on MCF-7 cell line with IC50 value of 1.75 to 9.58 µM. Compounds 5a, 6a, 6c, and 10c had weak toxicity towards normal HEK-293T, especially 10c displayed the highest IC50 with a value of 101.21 μM against normal cells. Furthermore, mechanistic studies for the antiproliferative activity were performed on the most active compounds 5a, 6a, 6c, and 10c. Compound 6c exhibited significant inhibitory activity against CDK2 enzyme with IC50 value of 0.614 µM compared to R-roscovitine (IC50 = 0.533 µM) as a reference drug. Additionally, compounds 5a, 6a, 6c, and 10c have significant potency and selectivity for the COX-2 enzyme (IC50 = 0.058 – 0.089 µM) over COX-1 enzyme (IC50 = 9.7 – 11.6 µM) compared to celecoxib and indomethacin. Accordingly, compounds 5a and 6c showed potent COX-2 inhibitory activity with IC50 values of 0.058 and 0.075 µM with a selectivity index of 198.27 and 154.66, respectively, in comparison to celecoxib and indomethacin with COX-2 IC50 value of 0.046 and 0.079 µM and a selectivity index of 315.21 and 1.25. compound 6c, with the potent CDK2 and COX-2 inhibitory activity, demonstrated apoptotic activity on HepG-2 cancer cells by inducing a strong G1 phase cell cycle arrest. Also, compound 6c significantly elevated the Bax/Bcl-2 ratio by 14.54 folds compared to the untreated control, which is clearly correlated with its sensitivity to apoptosis. Molecular docking and dynamics simulations were conducted to illustrate the binding modes inside the active sites. Finally, the hit compound 6c was discovered to have antiproliferative activity against HepG-2, MCF-7, and HCT-116 cancer cell lines by inhibiting CDK2 and COX-2 enzymes as proposal mechanisms.

The anti-breast cancer activity of indeno[1,2-b]pyridin-5-one and their hydrazonal precursors endowed with anti-CDK-2 enzyme activity

A new series of aza-indeno[1,2-b]pyridin-5-one derivatives 6a-h was designed. The novel pyridin-5-one derivatives were constructed via cyclization of their corresponding hydrazonal precursors 4a-h with indandione. Structural elucidation of all new compounds was fully conducted. All novel hydrazonals 4a-h and indeno-pyridinone derivatives 6a-h were screened for their anti-breast cancer activity against two cell lines; MCF-7 and MDA-231. Among all screened compounds, hydrazonals 4a and 4h showed the highest cytotoxic potency. The cell cycle analysis data revealed that hydrazonals 4a and 4h caused a 1.36- and 1.2-fold increase in the proportion of cells in S phase. Annexin V-FITC apoptosis test for the same two hydrazonal derivatives 4a and 4h indicated that these molecules induce apoptosis by means of the programmed cell death pathway rather than the necrotic pathway. Pharmacokinetic parameters of these two hydrazonals as well as their molecular docking study with the CDK-2 enzyme, provided more insights of their biological activity and druggability.

Synthesis and Anti-Breast Cancer Potency of Mono- and Bis-(pyrazolyl[1,2,4]triazolo[3,4-b][1,3,4]thiadiazine) Derivatives as EGFR/CDK-2 Target Inhibitors.

The target mono- and bis-(6-pyrazolyltriazolo-thiadiazine) derivatives 4a-c and 6a-d were synthesized using a straightforward protocol via reaction of 3-bromoacetylpyrazole 2 with 4-amino-s-triazole-3-thiols 3a-c and bis(4-amino-5-mercapto-s-triazol-3-yl)alkanes 5a-d, respectively. The bis(6-pyrazolyl-s-triazolo[3,4-b][1,3,4]thiadiazine) derivatives 8a,b and 10 were also constructed by reaction of the triazolo[3,4-b][1,3,4]thiadiazine-3-thiol 4c with the proper dibromo compounds 7a,b and 9, respectively. Structures of the new substances were determined by spectroscopic and analytical data. Compounds 4b, 4c, and 6a showed potent cytotoxicity against MCF-7 (IC50 = 3.16, 2.74, and 0.39 μM, respectively) and were safe against the MCF-10A cells. Compounds 4b, 4c, and 6a also showed promising dual EGFR and CDK-2 inhibition activities, particularly 6a was the most effective (IC50 = 19.6 and 87.9 nM, respectively), better than Erlotinib and Roscovitine. Compound 6a treatment induced EGFR and CDK-2 enzyme inhibition by 97.18% and 94.11%, respectively, at 10 μM (the highest concentration). Compound 6a notably induced cell apoptosis in MCF-7 cells, increasing the cell population by total apoptosis 43.3% compared to 1.29% for the untreated control group, increasing the cell population at the S-phase by 39.2% compared to 18.6% (control).

Novel [1,2,3]triazoles, [1,2,3]triazolo[4,5-d]Pyrimidines, and Some of Their Glycoside Derivatives: Synthesis and Molecular Modeling as Potential Apoptotic Antitumor Agents

Two new series of 4,5-difunctionalized 1-bromobenzyl[1,2,3]triazole (2a, 3a, 4a, 5a, and 6a) and 4,5-difunctionalized 1-(2-oxo-2-(p-tolylamino)ethyl-[1,2,3]triazole (2b, 3b, 4b, 5b, and 6b) were synthesized using related 1-(azidomethyl)-4-bromobenzene 1a and p-tolylcarbamoyl azide 1b respectively. The substituted [1,2,3]triazolo[4,5-d]pyrimidine-7-one derivatives (7a, 7b, 8a, and 8b) were synthesized by the reaction of [1,2,3]triazolo derivatives 2a and 2b with carbon disulfide in the presence of 10% sodium hydroxide/dimethylformamide and/or by the reaction with formic acid respectively. The S-glucoside derivatives (9–12) of newly synthesized [1,2,3]triazolo[4,5-d]pyrimidines were also synthesized. By using several spectroscopic methods, including IR, 1H NMR, 13C NMR, and elemental analysis, the chemical structures of the novel derivatives were confirmed. The synthetic compounds’ cytotoxicity and in vitro anticancer activity were examined vs. human breast carcinoma (MCF-7), human laryngeal carcinoma (HEP-2), and human colorectal carcinoma (HCT-116) cell lines. According to the findings, HEP-2 and HCT-116 cells are more sensitive to the tested compounds than the other cell lines. In the HEP-2 and MCF-7 cell lines, respectively, compounds 5b and 11 showed potential anticancer activity when compared to the effect of the commonly used anticancer medication, doxorubicin. The selectivity of compounds against the cancer cell line was confirmed by testing their cytotoxicity on VERO (African Green Monkey kidney) normal cells. The anticancer activity of those compounds is suggested to be due to nuclear damage generated by a high generation of reactive oxygen species (ROS). In addition, the induction of apoptosis by significantly upregulating the apoptotic genes PAR-4 and BAX while substantially downregulating the anti-apoptotic genes BCL-2 and BCL-xl. Molecular docking research was undertaken to predict the probable binding poses of the most effective drugs in the active site of CDK-2. The more active compounds (2a, 3a,b, 4a,b, 5a,b, 6b, 11, and 12) have been docked on the CDK-2 enzyme to demonstrate their mode of action as anticancer medicines. The compounds exert many interactions and showed high binding to the CDK-2 receptor. Finally, a hypothetical pharmacophore model was created using the Molecular Operating Environment (MOE) software and five compounds that are structurally similar to the synthesized ones with known anticancer action.

Flavonoids from Extract Butanol of Twigs Erythrina crista-galli Against the Breast Cancer Cell Line Within In Silico Method

Breast cancer is one of the most serious health problems in the world. The common treatments for breast cancer have side effects and resistance, so the search for cancer drugs from natural products that are more effective is still a concern for researchers. Flavonoids from Erythrina crista-galli, which is one of the natural products, have the potential as anticancer drugs based on their phytoestrogen activity that has been reported. The aim of this research is to isolate flavonoids from extract butanol of E. crista-galli with column chromatography and determine their anticancer activity by the in silico molecular docking method. Two flavonoid compounds with the names 6,8-diprenylgenistein from the isoflavone group and phaseolin from the pterocarpan group were isolated. Molecular docking analysis showed that the highest binding affinity values for compounds 1 and 2 were to CDK-2 protein with values of −10.14 and −8.8 kcal/mol, respectively. However, it is also possible to suggest inhibition through ER protein, especially in compound 1, with a value of −10.66 kcal/mol. Therefore, inhibition of the target CDK-2 enzyme is the most promising for the development of new drugs. HIGHLIGHTS Flavonoids have been isolated from butanol extract 6,8-diprenylgenistein and phaseolin were first reported from the species Erythrina crista-galli 6,8-diprenylgenistein has the potential as a new drug candidate with the highest stability based on its ΔG value by targeting the CDK-2 protein within in silico method GRAPHICAL ABSTRACT

A Computational Study of the Immobilization of New 5-Nitroisatine Derivatives with the Use of C60-Based Functionalized Nanocarriers

Isatin-based compounds are a large group of drugs used as competitive inhibitors of ATP. The 5-nitroisatin derivatives studied in this work are inhibitors of the CDK2 enzyme, which can be used in the development of new anti-cancer therapies. One of the basic activities that often allows for an increase in biological activity while reducing the undesirable effects associated with the toxicity of medicinal substances is immobilization based on carriers. In this work, fifty nanocarriers derived from C60 fullerene, containing a bound phenyl ring on their surfaces, were used in the process of the immobilization of isatin derivatives. Based on flexible docking methods, the binding capacities of the drugs under consideration were determined using a wide range of nanocarriers containing symmetric and asymmetric modifications of the phenyl ring, providing various types of interactions. Based on the data collected for each of the tested drugs, including the binding affinity and the structure and stability of complexes, the best candidates were selected in terms of the type of substituent that modified the nanoparticle and its location. Among the systems with the highest affinity are the dominant complexes created by functionalized fullerenes containing substituents with a symmetrical location, such as R2-R6 and R3-R5. Based on the collected data, nanocarriers with a high potential for immobilization and use in the development of targeted therapies were selected for each of the tested drugs.

Design, synthesis, crystal structures and biological evaluation of some 1,3-thiazolidin-4-ones as dual CDK2/EGFR potent inhibitors with potential apoptotic antiproliferative effects

A series of novel thiazolidine-4-one derivatives was synthesized by reacting 1,4-disubstituted hydrazine carbothioamides with diethyl azodicarboxylate. The structures were confirmed by spectroscopic data as well as single-crystal X-ray analyses. The antiproliferative activity of the synthesized compounds was investigated against four human cancer cell lines using an MTT assay. Compounds 5d, 5e, and 5f revealed the most potent antiproliferative activity with GI50 values ranging from 0.70 µM to 1.20 µM, compared to doxorubicin GI50 value = 1.10 µM. Compounds 5d, 5e, and 5f were further investigated for their inhibitory activities against CDK2 and EGFR as potential targets for their molecular mechanism. Compounds 5e and 5f have showed potent inhibitory activity to CDK2 enzyme with IC50 values of 18 and 14 nM, which is more potent than the reference dinaciclib (IC50 = 20 nM). Moreover, compounds 5e and 5f were the most potent EGFR inhibitors, with IC50 values of 93 and 87 nM, respectively, compared to the reference erlotinib (IC50 = 70 nM). In addition, the most potent derivatives were tested for their apoptotic activity against caspases 3, 8, and 9, and the results showed that compounds 5d, 5e, and 5f revealed a greater increase in active caspases 3,8 and 9 than doxorubicin. Also, compounds 5d, 5e, and 5f elevated cytochrome C levels in the MCF-7 human breast cancer cell line by about 15.5, 15.8, and 16.5 times, respectively. Finally, a molecular docking study was performed to investigate the binding sites of these compounds within the active sites of CDK2 and EGFR targets, and the results confirmed that the most potent CDK2 and EGFR inhibitor 5h also have showed the highest docking score.

Designing and Synthesis of New Isatin Derivatives as Potential CDK2 Inhibitors.

Tumors are still one of the main causes of death; therefore, the search for new therapeutic agents that will enable the implementation of effective treatment is a significant challenge for modern pharmacy. One of the important factors contributing to the development of neoplastic diseases is the overexpression of enzymes responsible for the regulation of cell division processes such as cyclin-dependent kinases. Numerous studies and examples of already-developed drugs confirm that isatin is a convenient basis for the development of new groups of inhibitors for this class of enzyme. Therefore, in this work, a new group of potential inhibitors of the CDK2 enzyme, utilizing isatin derivatives and substituted benzoylhydrazines, has been designed based on the application of computational chemistry methods, such as docking and molecular dynamics, and their inhibiting ability was assessed. In the cases of the selected compounds, a synthesis method was developed, and the selected physicochemical properties of the newly synthesized derivatives were estimated. As part of the completed project, new compounds are developed which are potential inhibitors of the CDK2 enzyme.

Abstract 5949: Aspirins metabolites inhibit human colon cancer cell growth: Potential role in colorectal cancer prevention

Abstract Aspirin’s role in colorectal cancer (CRC) prevention is evidential from several epidemiological data. Numerous theories and targets have been proposed, a consensus has not been reached regarding its mechanism of action. One of the unexplored area in aspirin’s CRC prevention is the role of Dihydroxy benzoic acids (DHBAs), which are generated from aspirin’s metabolism by gut microflora and cytochrome P450 (CYP450). Out of the screened DHBAs, 2,3-DHBA and 2,5-DHBA showed concentration dependent inhibition of CDK1, CDK2, CDK4 and CDK6 enzyme activity in-vitro. We demonstrated that 2,3-DHBA and 2,5-DHBA inhibits CDK-1 enzyme activity beginning at 500 µM, while CDK2 and CDK4 activity was inhibited only at higher concentrations (>750 µM). 2,3-DHBA inhibited CDK6 enzyme activity from 250 µM, while 2,5-DHBA inhibited its activity >750 µM. Using colony formation assays, we further demonstrated the role of 2,3-DHBA and 2,5-DHBA in cancer cell cycle inhibition in 3 different cancer cell lines. Out of the 2 DHBAs, 2,5-DHBA was highly effective in inhibiting clonal formation in HCT-116 and HT-29 CRC cell lines (250-500 µM), and in the MDA-MB-231 breast cancer cell line (~100 µM); whereas both aspirin and salicylic acid failed to inhibit all four CDKs and colony formation. Based on the present results, it is suggested that 2,3-DHBA and 2,5-DHBA may contribute to the chemopreventive properties of aspirin, possibly through the inhibition of CDKs. The present data and the proposed mechanisms should open new areas for future investigations. Citation Format: Poojitha Tummala, Ranjini Sankaranarayanan, Rakesh Dachineni, Jayarama Gunaje Bhat. Aspirins metabolites inhibit human colon cancer cell growth: Potential role in colorectal cancer prevention [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5949.

New cell cycle checkpoint pathways regulators with 2-Oxo-indoline scaffold as potential anticancer agents: Design, synthesis, biological activities and in silico studies

3-Arylidene-2-oxo-indoline derivatives are at the heart of a wide range of clinically, medicinally and biologically important compounds among the 2-oxo-indolines. A number of 3-arylidene-2-oxo-indolines have been approved for clinical application. Accordingly, the current work describes the structural based design of 3-arylidene-2-oxindole derivatives through docking of their structures in the active site of CDK2 as one of the dominant enzyme checkpoints. Based on the docking studies a range of 3-arylidene-2-oxindole derivatives, 5(a-n) and 6(a-x), with variable substituents at positions 1 and 5 of the 2-oxindole as well as 3 and 4 of the aryl moieties were synthesized. These molecules exist in either E or Z diastereomer about the exocyclic double bond at position 3 of oxindole nucleus. Their structures were confirmed by spectral and elemental methods of analyses and the E/Z-configuration of the diastereomers was confirmed by 2D NOE analysis. In vitro cytotoxicity of these molecules was tested against four cancerous cell lines, namely, breast cancer cell line (MCF7), liver carcinoma cell line (HepG2), cervix carcinoma cell line (HeLa), colon cancer cell line (HCT116) in addition to the diploid human normal non-cancerous cell line (F180) using SRB and MTT assays. The tested molecules showed variable cytotoxic effects on the four cancer cell lines with pronounced selectivity compared to the normal one (F180) with no significant difference between E and Z diastereomers. Compounds 5a, 5b, 5e1, 5m, 6f and 6j were tested for the effect on the expression on CDK2, p53, caspase-3 and caspase-9 proteins, and revealed variable activities compared to the positive controls Sunitinib and Staurosporine. These molecules seem to have multiple cellular targets as they induced expression of p53 and caspases while inhibited that of CDK2. Apoptotic effect of compound 6j was further investigated using annexin V-FITC/PI dual staining assay and showed that cells treated with 6j have nearly 15 folds greater apoptotic effect than that of the control cells. Furthermore, inhibitory activity of compounds 5a, 5b, 5e1, 5m, 6f and 6j on CDK2 enzyme were tested and revealed that compound 6f, with the N-4-flourobenzyl- 2-oxindole and 3-p-chlorobenzylidene moieties, has a comparable inhibitory activity to the reference drug sunitinib.

Discovery of New Pyrazolopyridine, Furopyridine, and Pyridine Derivatives as CDK2 Inhibitors: Design, Synthesis, Docking Studies, and Anti-Proliferative Activity.

New pyridine, pyrazoloyridine, and furopyridine derivatives substituted with naphthyl and thienyl moieties were designed and synthesized starting from 6-(naphthalen-2-yl)-2-oxo-4-(thiophen-2-yl)-1,2-dihydropyridine-3-carbonitrile (1). The chloro, methoxy, cholroacetoxy, imidazolyl, azide, and arylamino derivatives were prepared to obtain the pyridine-−C2 functionalized derivatives. The derived pyrazolpyridine-N-glycosides were synthesized via heterocyclization of the C2-thioxopyridine derivative followed by glycosylation using glucose and galactose. The furopyridine derivative 14 and the tricyclic pyrido[3′,2′:4,5]furo[3,2-d]pyrimidine 15 were prepared via heterocyclization of the ester derivative followed by a reaction with formamide. The newly synthesized compounds were evaluated for their ability to in vitro inhibit the CDK2 enzyme. In addition, the cytotoxicity of the compounds was tested against four different human cancer cell lines (HCT-116, MCF-7, HepG2, and A549). The CDK2/cyclin A2 enzyme inhibitory results revealed that pyridone 1, 2-chloro-6-(naphthalen-2-yl)-4-(thiophen-2-yl)nicotinonitrile (4), 6-(naphthalen-2-yl)-4-(thiophen-2-yl)-1H-pyrazolo[3,4-b]pyridin-3-amine (8), S-(3-cyano-6-(naphthaen-2-yl)-4-(thiophen-2-yl)pyridin-2-yl) 2-chloroethanethioate (11), and ethyl 3-amino-6-(naphthalen-2-yl)-4-(thiophen-2-yl)furo[2,3-b]pyridine-2-carboxylate (14) are among the most active inhibitors with IC50 values of 0.57, 0.24, 0.65, 0.50, and 0.93 µM, respectively, compared to roscovitine (IC50 0.394 μM). Most compounds showed significant inhibition on different human cancer cell lines (HCT-116, MCF-7, HepG2, and A549) with IC50 ranges of 31.3–49.0, 19.3–55.5, 22.7–44.8, and 36.8–70.7 μM, respectively compared to doxorubicin (IC50 40.0, 64.8, 24.7 and 58.1 µM, respectively). Furthermore, a molecular docking study suggests that most of the target compounds have a similar binding mode as a reference compound in the active site of the CDK2 enzyme. The structural requirements controlling the CDK2 inhibitory activity were determined through the generation of a statistically significant 2D-QSAR model.

Design, Synthesis, Anticancer Evaluation, Enzymatic Assays, and a Molecular Modeling Study of Novel Pyrazole-Indole Hybrids.

The molecular hybridization concept has recently emerged as a powerful approach in drug discovery. A series of novel indole derivatives linked to the pyrazole moiety were designed and developed via a molecular hybridization protocol as antitumor agents. The target compounds (5a–j and 7a–e) were prepared by the reaction of 5-aminopyrazoles (1a–e) with N-substituted isatin (4a,b) and 1H-indole-3-carbaldehyde (6), respectively. All products were characterized via several analytical and spectroscopic techniques. Compounds (5a–j and 7a–e) were screened for their cytotoxicity activities in vitro against four human cancer types [human colorectal carcinoma (HCT-116), human breast adenocarcinoma (MCF-7), human liver carcinoma (HepG2), and human lung carcinoma (A549)] using the MTT assay. The obtained results showed that the newly synthesized compounds displayed good-to-excellent antitumor activity. For example, 5-((1H-indol-3-yl)methyleneamino)-N-phenyl-3-(phenylamino)-1H-pyrazole-4-carboxamide (7a) and 5-((1H-indol-3-yl)methyleneamino)-3-(phenylamino)-N-(4-methylphenyl)-1H-pyrazole-4-carboxamide (7b) provided excellent anticancer inhibition performance against the HepG2 cancer cell line with IC50 values of 6.1 ± 1.9 and 7.9 ± 1.9 μM, respectively, compared to the standard reference drug, doxorubicin (IC50 = 24.7 ± 3.2 μM). The two powerful anticancer compounds (7a and 7b) were further subjected to cell cycle analysis and apoptosis investigation in HepG2 using flow cytometry. We have also studied the enzymatic assay of these two compounds against some enzymes, namely, caspase-3, Bcl-2, Bax, and CDK-2. Interestingly, the molecular docking study revealed that compounds 7a and 7b could well embed in the active pocket of the CDK-2 enzyme via different interactions. Overall, the prepared pyrazole–indole hybrids (7a and 7b) can be proposed as strong anticancer candidate drugs against various cancer cell lines.

Development of isatin-thiazolo[3,2-a]benzimidazole hybrids as novel CDK2 inhibitors with potent in vitro apoptotic anti-proliferative activity: Synthesis, biological and molecular dynamics investigations

In the current medical era, human health is experiencing numerous challenges, particularly the human malignancies. Therefore, the therapeutic arsenal for these malignancies is to be inexorably enhanced with new treatments that target tumor cells in a selective manner. In this regard, the present work aims at developing a new set of small molecules featuring the privileged isatin scaffold conjugated with a thiazolo[3,2-a]benzimidazole (TBI) motif through a cleavable hydrazide linker (7a-e and 10a-i) as potential anticancer CDK2 inhibitors. The large tricyclic TBI motif is anticipated to achieve a plethora of hydrophobic interactions within the CDK2 binding site. The growth of the two examined cell lines was significantly inhibited by most the prepared hybrids with IC50 ranges; (2.60 ± 1.47–20.90 ± 1.17 µM, against MDA-MB-231) and (1.27 ± 0.06–16.83 ± 0.95 µM, against MCF-7). In particular, hybrids 7a, 7d and 10a displayed potent dual activity against the examined cell lines, and thus selected for further investigations. They exerted a significance alteration in the cell cycle progression, in addition to an apoptosis induction within both MDA-MB-231 and MCF-7 cells. Furthermore, 7a, 7d and 10a displayed potent CDK2 inhibitory action (IC50 = 96.46 ± 5.3, 26.24 ± 1.4 and 42.95 ± 2.3 nM, respectively). The docking simulations unveiled, as expected, the ability of the TBI ring to well-accommodate and establish several hydrophobic interactions within a hydrophobic pocket in the CDK2 binding site. Also, the docking simulations highlighted the significance of incorporation of the hydrazide linker and isatin unsubstituted (NH) functionality in the H-bonding interactions. Interestingly, the most potent CDK2 inhibitor 7d achieved the best binding score (-11.2 Kcal/mole) and formed the most stable complex with CDK2 enzyme (RMSD = 1.24 Å) in a 100 ns MD simulation. In addition, the MM-PBSA calculations ascribed the lowest binding free energy to the 7d–CDK2 complex (−323.69 ± 15.17 kJ/mol). This could be attributed to an incorporation of the 5-OCH3 group that was engaged in an extra hydrogen bonding with key THR14 amino acid residue. Finally, these results suggested hybrid 7d as a good candidate for further optimization as promising breast cancer antitumor agent and CDK2 inhibitor.

Tetrahydroindazole inhibitors of CDK2/cyclin complexes

Over 50 tetrahydroindazoles were synthesized after 7-bromo-3,6,6-trimethyl-1-(pyridin-2-yl)-5,6,7,7a-tetrahydro-1H-indazol-4(3aH)-one (3) was identified as a hit compound in a high throughput screen for inhibition of CDK2 in complex with cyclin A. The activity of the most promising analogues was evaluated by inhibition of CDK2 enzyme complexes with various cyclins. Analogues 53 and 59 showed 3-fold better binding affinity for CDK2 and 2- to 10-fold improved inhibitory activity against CDK2/cyclin A1, E, and O compared to screening hit 3. The data from the enzyme and binding assays indicate that the binding of the analogues to a CDK2/cyclin complex is favored over binding to free CDK2. Computational analysis was used to predict a potential binding site at the CDK2/cyclin E1 interface.

Novel oxindole/benzofuran hybrids as potential dual CDK2/GSK-3β inhibitors targeting breast cancer: design, synthesis, biological evaluation, and in silico studies

The serine/threonine protein kinases CDK2 and GSK-3β are key oncotargets in breast cancer cell lines, therefore, in the present study three series of oxindole-benzofuran hybrids were designed and synthesised as dual CDK2/GSK-3β inhibitors targeting breast cancer (5a–g, 7a–h, and 13a–b). The N1 -unsubstituted oxindole derivatives, series 5, showed moderate to potent activity on both MCF-7 and T-47D breast cancer cell lines. Compounds 5d–f showed the most potent cytotoxic activity with IC50 of 3.41, 3.45 and 2.27 μM, respectively, on MCF-7 and of 3.82, 4.53 and 7.80 μM, respectively, on T-47D cell lines, in comparison to the used reference standard (staurosporine) IC50 of 4.81 and 4.34 μM, respectively. On the other hand, the N1 -substituted oxindole derivatives, series 7 and 13, showed moderate to weak cytotoxic activity on both breast cancer cell lines. CDK2 and GSK-3β enzyme inhibition assay of series 5 revealed that compounds 5d and 5f are showing potent dual CDK2/GSK-3β inhibitory activity with IC50 of 37.77 and 52.75 nM, respectively, on CDK2 and 32.09 and 40.13 nM, respectively, on GSK-3β. The most potent compounds 5d–f caused cell cycle arrest in the G2/M phase in MCF-7 cells inducing cell apoptosis because of the CDK2/GSK-3β inhibition. Molecular docking studies showed that the newly synthesised N1 -unsubstituted oxindole hybrids have comparable binding patterns in both CDK2 and GSK-3β. The oxindole ring is accommodated in the hinge region interacting through hydrogen bonding with the backbone CO and NH of the key amino acids Glu81 and Leu83, respectively, in CDK2 and Asp133 and Val135, respectively, in GSK-3β. Whereas, in series 7 and 13, the N1 -substitutions on the oxindole nucleus hinder the compounds from achieving these key interactions with hinge region amino acids what rationalises their moderate to low anti-proliferative activity.

In silico design and molecular docking study of CDK2 inhibitors with potent cytotoxic activity against HCT116 colorectal cancer cell line

BackgroundColorectal cancer is common to both sexes; third in terms of morbidity and second in terms of mortality, accounting for 10% and 9.2% of cancer cases in men and women globally. Although drugs such as bevacizumab, Camptosar, and cetuximab are being used to manage colorectal cancer, the efficacy of the drugs has been reported to vary from patient to patient. These drugs have also been reported to have varying degrees of side effects; thus, the need for novel drug therapies with better efficacy and lesser side effects. In silico drugs design methods provide a faster and cost-effect method for lead identification and optimization. The aim of this study, therefore, was to design novel imidazol-5-ones via in silico design methods. ResultsA QSAR model was built using the genetic function algorithm method to model the cytotoxicity of the compounds against the HCT116 colorectal cancer cell line. The built model had statistical parameters; R2 = 0.7397, R2adj = 0.6712, Q2cv = 0.5547, and R2ext. = 0.7202 and revealed the cytotoxic activity of the compounds to be dependent on the molecular descriptors nS, GATS5s, VR1_Dze, ETA_dBetaP, and L3i. These molecular descriptors were poorly correlated (VIF < 4.0) and made unique contributions to the built model. The model was used to design a novel set of derivatives via the ligand-based drug design approach. Compounds e, h, j, and l showed significantly better cytotoxicity (IC50 < 5.0 μM) compared to the template. The interaction of the compounds with the CDK2 enzyme (PDB ID: 6GUE) was investigated via molecular docking study. The compounds were potent inhibitors of the enzyme having binding affinity of range −10.8 to −11.0 kcal/mol and primarily formed hydrogen bond interaction with lysine, aspartic acid, leucine, and histidine amino acid residues of the enzyme. ConclusionThe QSAR model built was stable, robust, and had a good predicting ability. Thus, predictions made by the model were reliably employed in further in silico studies. The compounds designed were more active than the template and showed better inhibition of the CDK2 enzyme compared to the standard drugs sorafenib and kenpaullone.

Synthesis and Bioactivity Evaluation of Indole-Thiophene polymer with Molecular Docking Studies

Emulsion polymerization of 2-amino-4-(1-benzyl-1H-indol-3-yl) thiophene-3-carbonitrile (ABITC) using ammonium persulfate (APS) as an oxidizing agent afforded two isomers of poly (2-amino-4-(1-benzyl-1H-indol-3-yl) thiophene-3-carbonitrile) (PABITC) with high molecular weight 35673 and 28596 g/mol. Chemical structure and morphology of the newly synthesized polymers were investigated by IR, 1HNMR, SEM, and GPC. Nano capsulation of ABITC, PABITC, and PABITC/Doxorubicin by polyethylene glycol (PEG) was achieved by the nano-precipitation method. The anti-proliferative activity of the newly synthesized PABITC and nano-capsulation against HepG2, Huh7, and A549 cancer cell lines were investigated using MTT assay. The result obtained indicates that the encapsulation of ABITC inside PEG-NP led to an improvement in their anti-proliferative activity against cancer cell lines compared to free ABITC. The free PABITC revealed moderate anti-proliferative activity against tested cells and their encapsulation form with PEG-NP revealed no significant change in the activity with the fold changed not exceed 1-time fold. Furthermore, the anti-proliferative activity of PABITC -NP was improved after Doxorubicin (DOX) encapsulation against tested cells compared to PABITC - PEG-NP. In addition, PABITC exhibited potent antibacterial activity against tested microbes comparing to monomer ABITC and the reference drug amikacin. Moreover, the binding mode of the monomer ABITC beside two repeated units of monomer inside the active site of the DNA gyrase B chain (PDB ID: 1KIJ) as promising bacterial target and CDK2 enzyme (PDB ID: 1PYE)] as promising cancer target was studied using molecular docking technique.

Potential Anticancer role of Leonurine and its Derivatives

Cancer is disease characterized by uncontrolled cell division and the ability of the cells to attack other biological tissues. Leonurine is a compound obtained from the Siberian motherwort (Leonurus artemisia L.) that can inhibit cancer cells growth. The discovery of this compound by means of synthesis has been developed using computational chemistry. One of the techniques that have been developed is in silico method. The purposes of this study were to find out the ability of leonurine and its derivatives to eliminate the Cyclin-Dependent Kinase-2 (CDK-2 enzyme) as a requirement for anticancer agents and to find out whether leonurine and its derivatives are good substances for anticancer drugs. Leonurine derivatives were formed using ChemDraw Ultra 8.0, HyperChem, Open Babel 2.3.2, then docked using AutoDock 4.2, and visualized using Discovery Studio Visualizer in order to see the interaction between macromolecular ligands and CDK-2 obtained from (Protein Data Bank) PDB sites. From the in silico study, 15 derivatives of leonurine were found and the derivative-9 has good potential as candidate for anticancer drug with Energy Binding (ΔG) values of -7.81 kcal/mol.

Novel Pyrazolo[3,4-d]pyrimidines as Potential Cytotoxic Agents: Design, Synthesis, Molecular Docking and CDK2 Inhibition.

Pyrazolo[3,4-d]pyrimidine scaffold was reported to possess potent cytotoxic and CDK2 inhibitory activity as analogue of roscovitine. To design and synthesize novel 1-(4-flourophenyl)pyrazolo[3,4-d]pyrimidine derivatives as bioisosters of roscovitine with potential cytotoxic and CDK2 inhibitory activity. A series of novel 1-(4-flourophenyl)pyrazolo[3,4-d]pyrimidines were designed and synthesized. Structural elucidation for all the newly synthesized compounds was achieved through performing MS, 1H NMR, 13C NMR and IR spectral techniques. Eight compounds were screened for their cytotoxic activity by National Cancer Institute (USA) against 60 different human cancer cell lines. Compounds 2a, 4, 6, 7b, 8a and 8b were further studied through the determination of their IC50 values against the most sensitive cell lines. The inhibitory activities of compounds 2a and 4 were evaluated against CDK2 enzyme. Compound 4 exhibited the most prominent broad-spectrum cytotoxic activity against 42 cell lines representing all human cancer types showing growth inhibition percentages from 53.19 to 99.39. Compound 2a showed promising selectivity against several cell lines. Moreover, all the test compounds exhibited potent cytotoxic activity in nanomolar to micromolar range with IC50 values ranging from 0.58 to 8.32μM. Compound 2a showed significant cytotoxic activity against CNS (SNB-75), lung (NCI-H460) and ovarian (OVCAR-4) cancer cell lines with IC50 values 0.64, 0.78 and 1.9μM, respectively. Compound 4 showed promising potency against leukemia (HL-60) and CNS (SNB-75) cell lines (IC50 = 0.58 and 0.94μM, sequentially). Moreover, the antiproliferative activities of compounds 2a and 4 appeared to correlate well with their ability to inhibit CDK2 at sub-micromolar level (IC50 = 0.69 and 0.67μM, respectively) that were comparable to roscovitine (IC50=0.44μM). The Molecular docking results revealed that compound 4 interacted with the same key amino acids as roscovitine in the active site of CDK2 enzyme with a marked docking score (-14.1031 kcal/mol). 1-(4-Flourophenyl)pyrazolo[3,4-d]pyrimidine is a promising scaffold for the design and synthesis of potent cytotoxic leads.