Exploring new quinazolin-4(3H)-one derivatives as CDK2 inhibitors: Design, synthesis, and anticancer evaluation

In the present work, five series of new 2,3-disubstituted quinazolin-4(3H)-ones 4a-c, 5a-d, 6a-g, 7a,b, and 9a-c were designed, synthesized, and screened in vitro for their cytotoxic activity against 60 cancer cell lines by the National Cancer Institute, USA. Five candidates 4c, 6a, 6b, 6d, and 6g revealed promising cytotoxicity with significant percentage growth inhibition in the range of 81.98%-96.45% against the central nervous system (CNS) (SNB-19), melanoma (MDA-MB-435), and non-small cell lung cancer (HOP-62) cell lines. The in vitro cytotoxic half maximal inhibitory concentration (IC50 ) values for the most active compounds 4c, 6a, 6b, 6d, and 6g against the most sensitive cell lines were evaluated. Additionally, screening their cyclin-dependent kinase 2 (CDK2) inhibitory activity was performed. Ortho-chloro-benzylideneamino derivative 6b emerged as the most potent compound with IC50  = 0.67 µM compared to Roscovitine (IC50  = 0.64 µM). The most active candidates arrested the cell cycle at G1, S phases, or both, leading to cell death and inducing apoptosis against CNS (SNB-19), melanoma (MDA-MB-435), and non-small cell lung cancer (HOP-62) cell lines. The molecular docking study verified the resulting outcomes for the most active candidates in the CDK2-binding pocket. Finally, physicochemical, and pharmacokinetic properties deduced that compounds 4c, 6a, 6b, 6d, and 6g displayed significant drug-likeness properties. According to the obtained results, the newly targeted compounds are regarded as promising scaffolds for the continued development of novel CDK2 inhibitors.

Cancer takes many paths through G1/S

In the commonly accepted paradigm for control of the mammalian cell cycle, sequential cyclin-dependent kinase (CDK) and cyclin activities drive the orderly transition from G1 to S phase. However, recent studies using different technological approaches and examining a broad range of cancer cell types are challenging this established paradigm. An alternative model is evolving in which cell cycles utilize different drivers and take different trajectories through the G1/S transition. We are discovering that cancer cells in particular can adapt their drivers and trajectories, which has important implications for antiproliferative therapies. These studies have helped to refine an understanding of how CDK inhibition impinges on proliferation and have significance for understanding fundamental features of cell biology and cancer.

Synthesis and biological evaluation of novel pteridin-7(8H)-one derivatives as potent CDK2 inhibitors

Cyclin-dependent kinase 2 (CDK2) is considered as an important target in the research of antitumor drugs. Taking the CDK2/4/6 inhibitor Ebvaciclib as the positive control and an in-house library compound (23) as the lead compound, three classes of 30 target compounds with pteridin-7(8H)-one as the core structure were designed to establish structure-activity relationships (SAR). In general, SAR of pteridin-7(8H)-one CDK2 inhibitors is systematically described in this paper, resulting in the discovery of two compounds (KII-17 and KII-21) with further research value. After the above compounds were tested for CDK2/4/6 kinase selectivity, we found that compound KII-21 was about 3 and 4 times more selective to CDK2-cyclinE2 than CDK4-cyclinD1 and CDK6-cyclinD3, respectively. This work also provides a reference basis for the subsequent research on CDK2 inhibitors.

kinCSM: Using graph-based signatures to predict small molecule CDK2 inhibitors

Protein phosphorylation acts as an essential on/off switch in many cellular signaling pathways. This has led to ongoing interest in targeting kinases for therapeutic intervention. Computer‐aided drug discovery has been proven a useful and cost‐effective approach for facilitating prioritization and enrichment of screening libraries, but limited effort has been devoted providing insights on what makes a potent kinase inhibitor. To fill this gap, here we developed kinCSM, an integrative computational tool capable of accurately identifying potent cyclin‐dependent kinase 2 (CDK2) inhibitors, quantitatively predicting CDK2 ligand–kinase inhibition constants (pK_i) and classifying different types of inhibitors based on their favorable binding modes. kinCSM predictive models were built using supervised learning and leveraged the concept of graph‐based signatures to capture both physicochemical properties and geometry properties of small molecules. CDK2 inhibitors were accurately identified with Matthew's Correlation Coefficients (MCC) of up to 0.74, and inhibition constants predicted with Pearson's correlation of up to 0.76, both with consistent performances of 0.66 and 0.68 on a nonredundant blind test, respectively. kinCSM was also able to identify the potential type of inhibition for a given molecule, achieving MCC of up to 0.80 on cross‐validation and 0.73 on the blind test. Analyzing the molecular composition of revealed enriched chemical fragments in CDK2 inhibitors and different types of inhibitors, which provides insights into the molecular mechanisms behind ligand–kinase interactions. kinCSM will be an invaluable tool to guide future kinase drug discovery. To aid the fast and accurate screening of CDK2 inhibitors, kinCSM is freely available at https://biosig.lab.uq.edu.au/kin_csm/.

Development of newly synthesised quinazolinone-based CDK2 inhibitors with potent efficacy against melanoma

Inhibiting Cyclin-dependent kinase 2 (CDK2) has been established as a therapeutic strategy for the treatment of many cancers. Accordingly, this study aimed at developing a new set of quinazolinone-based derivatives as CDK2 inhibitors. The new compounds were evaluated for their anticancer activity against sixty tumour cell lines. Compounds 5c and 8a showed excellent growth inhibition against the melanoma cell line MDA-MB-435 with GI% of 94.53 and 94.15, respectively. Cell cycle analysis showed that compound 5c led to cell cycle cessation at S phase and G2/M phase revealing that CDK2 could be the plausible biological target. Thus, the most cytotoxic candidates 5c and 8a were evaluated in vitro for their CDK2 inhibitory activity and were able to display significant inhibitory action. The molecular docking study confirmed the obtained results. ADME study predicted that 5c had appropriate drug-likeness properties. These findings highlight a rationale for further development and optimisation of novel CDK2 inhibitors.

Advances in Pyrazole Based Scaffold as Cyclin-Dependent Kinase 2 Inhibitors for the Treatment of Cancer

The transformation of a normal cell into a tumor cell is one of the initial steps in cell cycle deregulation. The cell cycle is regulated by cyclin-dependent kinases (CDKs) that belong to the protein kinase family. CDK2 is an enchanting target for specific genotypes tumors since cyclin E is selective for CDK2 and the deregulation of specific cancer forms. Thus, CDKs inhibitor specifically CDK2/cyclin A-E has the potential to be a valid cancer target as per the currently undergoing clinical trials. Mostly pyrazole scaffolds have shown selectivity and potency for CDK2 inhibitors. This review demonstrates pyrazole and pyrazole fused with other heterocyclic rings for anti-proliferative activity. Based on the in vitro and molecular docking studies, the IC50 value of various hybrids is revealed to display the most potent analogs for CDK2 inhibition. Thus, the review emphasizes various lead analogs of pyrazole hybrids which can be found to be very potent and selective for anti-cancer drugs.

Synthesis of a new series of pyrazolo[1,5-a]pyrimidines as CDK2 inhibitors and anti-leukemia

Based on the structural study of previously known CDK2 inhibitors, a new series of pyrazolo[1,5-a]pyrimidine derivatives was designed and synthesized. The target compounds were biologically assessed as potent CDK2 inhibitors and promising anti-leukemia hits. The 7-(4-Bromo-phenyl)-3-(3-chloro/2-chloro-phenylazo)-pyrazolo[1,5-a]pyrimidin-2-ylamines 5 h and 5i revealed the best CDK2 inhibitory activity with comparable potency (IC₅₀ = 22 and 24 nM, respectively) to that of dinaciclib (IC₅₀ = 18 nM). Additionally, both analogues showed potent activities against CDK1, CDK5 and CDK9 at nanomolar concentrations (IC₅₀ = 28-80 nM). The anti-leukemia screening of the target compounds showed strong to moderate cytotoxicity against the used leukemia cell lines (MOLT-4 and HL-60). Compound 5 h inhibited MOLT-4 and HL-60 by 1.4 and 2.3 folds (IC₅₀ = 0.93 and 0.80 µM), respectively, compared to dinaciclib (IC₅₀ = 1.30 and 1.84 µM). Furthermore, compound 5i was comparable to dinaciclib against MOLT-4 and exhibited twice its activity against HL-60. Besides, the cytotoxicity of the promising analogues on normal human blood cells indicated the safety of 5h and 5i as compared to the reference dinaciclib. The pharmacokinetic properties of 5h and 5i were predicted using ADME calculations revealing good oral bioavailability and high GI absorption. The molecular docking simulations indicated, as expected, that the dinaciclib analogues can well-accommodate the CDK2 binding site, forming a variety of interactions.

Discovery of 3,6-disubstituted pyridazines as a novel class of anticancer agents targeting cyclin-dependent kinase 2: synthesis, biological evaluation and in silico insights

Human health in the current medical era is facing numerous challenges, especially cancer. So, the therapeutic arsenal for cancer should be unremittingly enriched with novel small molecules that selectively target tumour cells with minimal toxicity towards normal cells. In this context, herein a new series of 3,6-disubstituted pyridazines 11a–r has been synthesised and evaluated for in vitro anticancer activity. They possessed good anti-proliferative action towards human breast cancer T-47D (IC₅₀ range: 0.43 ± 0.01 − 35.9 ± 1.18 µM) and MDA-MB-231 (IC₅₀ range: 0.99 ± 0.03 − 34.59 ± 1.13 µM) cell lines, whereas they displayed weak activity against the tested ovarian cancer cell line SKOV-3. Among the studied compounds, the methyltetrahydropyran-bearing pyridazine 11m emerged as the unique submicromolar growth inhibitor herein reported towards both T-47D (IC₅₀ = 0.43 ± 0.01 µM) and MDA-MB-231 (IC₅₀ = 0.99 ± 0.03 µM) cell lines. In addition, the biological results indicated that pyridazines 11l and 11m exerted an efficient alteration within the cell cycle progression as well as induction of apoptosis in both T-47D and MDA-MB-231 cells. Moreover, pyridazines 11l and 11m displayed good mean tumour S. I. values of 13.7 and 16.1 upon assessment of their cytotoxicity towards non-tumorigenic breast MCF-10A cells. Furthermore, an in silico study proposed CDK2 as a probable enzymatic target for pyridazines 11, and explored their binding interactions within the vicinity of CDK2 binding site. Subsequently, pyridazines 11e, 11h, 11l, and 11m were selected to be evaluated for their ability to inhibit CDK2, where they exerted good inhibitory activity (IC₅₀ = 151, 43.8, 55.6 and 20.1 nM, respectively). Finally, the in silico study implied that target pyridazines 11 exhibited not only an efficient anticancer activity but also an acceptable ADME, physicochemical and druglikeness properties, specifically pyridazines 11l and 11m. Overall the obtained results from this study quite sustained our strategy and gave us a robust opportunity for further development and optimisation of 3,6-disubstituted pyridazine scaffold to enrich therapeutic arsenal with efficient and safe anticancer CDK inhibitors.

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.

Synthesis of Novel Fluorine Compounds Substituted-4-thiazolidinones Derived from Rhodanine Drug as Highly Bioactive Probes

Aim and Objective:

It is known that rhodanine drug has various biocidal activities. The aim of this work was to improve the structure of rhodanine drug via alkylation at N, S, and O- centers in addition to the introduction of fluorine atoms. The new fluorinated modified rhodanines 2-16 were evaluated as enzymatic probes for cellobiase activity produced by fungi and as CDK2 inhibitors of tumor cells.

Materials and Methods:

Novel fluorine substituted N-alkyl, S-alkyl and amino-rhodanines were obtained via Hydroxy methylation, Mannich reactions, chlorination and amination of 5-(4'-fluorophenylene)-2-thioxo-thiazolidin-4-one, and the enzymatic effects of cellobiase produced by fungi and /or CDK2 inhibition of tumor cells were evaluated.

Results:

Most of the targets were obtained in high yield and in the form of very pure crystals with characteristic colors. Only compounds 5, 8, 10, 13, and 14 exhibited a higher activity as cellobiase while compounds 2 and 5 showed a highly enzymatic effect on tumor cells. In addition, compounds 2 and 10 can be used as Olomoucine (standard referees).

Conclusion:

Various N, S and O-alkyl derivatives of fluorine-substituted rhodanines were prepared via a simple method and used as enzymatic probes for cellobiase activity produced by fungi and CDK2 inhibitors for tumor cells. The more bioactive compounds had rich fluorine atoms as p-fluorophenyl and p-fluorobenzoyl bearing N, S, O-alkyl rhodanine. The highly active compounds may be used as enzymatic materials for various biological transformations in the future.

Interaction between somatic mutations and germline variants contributes to clinical heterogeneity in cancer

Deciphering principles of inter-tumoral heterogeneity is crucial for refinement of precision oncology. We have recently demonstrated that 'oncogenic cooperation' between somatic mutations and regulatory germline variants can serve as a major cause for inter-tumoral heterogeneity, suggesting the requirement of integrating the regulatory genome into 'omics'-based precision oncology.

Design, synthesis and molecular docking of novel pyrazolo[1,5-a][1,3,5]triazine derivatives as CDK2 inhibitors

Cyclin Dependent Kinases CDKs unpredictable activity has been accounted for a wide assortment of human malignancies, so it might be conceivable to design pharmacologically relevant ligands that go about as specific and potent inhibitors of CDK2 action. In this respect, a series of novel pyrazolo[1,5-a][1,3,5]triazine derivatives were designed, synthesized and evaluated for CDK2 enzyme inhibitory and anticancer activity. Compounds 9f and 10c showed best CDK2 inhibition among the newly synthesized compounds, with percent inhibition at 82.38%, and 81.96% against CDK2 and IC₅₀ of 1.85 and 2.09 µM, respectively. Additionally, the newly synthesized compounds were tested for their antiproliferative activity against 60 NCI cell lines. Molecular docking revealed the binding mode of these new compounds into the roscovitine binding site of CDK2 enzyme (PDB code: 3ddq). Conclusively, pyrazolotriazine derivatives represent a talented starting point for further study as anticancer drug.

Medicinal Chemistry Profiling of Monocyclic 1,2-Azaborines

The first examples of biologically active monocyclic 1,2-azaborines have been synthesized and demonstrated to exhibit not only improved in vitro aqueous solubility in comparison with their corresponding carbonaceous analogues, but in the context of a CDK2 inhibitor, also improved biological activity and better in vivo oral bioavailability. This proof-of-concept study establishes the viability of monocyclic 1,2-azaborines as a novel pharmacophore with distinct pharmacological profiles that can help address challenges associated with solubility in drug development research.