DNA Antimetabolites Research Articles

Decision Tree for Mechanism of Antitumor Drugs Action Prediction

Classification by the mechanism of action of antitumor drugs using quantitative descriptors has been carried out in this study. The dataset of drugs includes 115 compounds with known activity and mechanism of action. The structures have been taken from the National Cancer Institute database. The dataset includes: 30 structures with the mechanism of alkylation action, 23 compounds are topoisomerase I inhibitors, 16 structures are topoisomerase II inhibitors, 17 compounds are DNA/RNA antimetabolites (dihydrofolate reductase inhibitors), 16 molecules are DNA antimetabolites, and 13 compounds are antimitotic drugs. A decision tree has been constructed for determination of each class of the compounds using 3D descriptors that have been computed by MERA software. Analysis of the results has shown that each mechanism of drug action is characterized by a set of descriptors. Important quantum-chemical descriptors of structures with mechanism for alkylation action, DNA/RNA antimetabolites, and DNA antimetabolites have been determined. Quantum-chemical and geometric descriptors for structures of topoisomerase II inhibitors and geometric descriptors for structures of topoisomerase I inhibitors have been established. An important energy descriptor for antimitotic drugs has been determined. The typical descriptor values for active and inactive structures for each mechanism of action have been determined. The quality recognition of active structures for each mechanism of drugs action has been determined. The highest recognition quality value of active and inactive compounds is observed in the decision tree of topoisomerase II inhibitors. The minimal recognition quality value of active and inactive compounds is observed in the decision tree of DNA/RNA-antimetabolites. The suggested decision trees can be used for determination of the action mechanism of antitumor drugs.

An in silico approach for evaluating the antitumor and epigenetic modulating potential of phenolic compounds occurring in edible and medicinal mushrooms

Introduction: As part of cancer research, mycotherapy is a relatively new and promissory source of agents with immunomodulating and antitumor properties. Ongoing research projects are aiming to provide mushrooms as a new generation of "biotherapeutics". In addition to high-molecular weight polysaccharides, efforts should be made to find new anticancer drugs using low-molecular weight secondary metabolites, e.g. phenolic compounds that can inhibit or trigger specific biochemical signals leading to cancer. Methods: An in silico approach based on the structural similarity of low-molecular weight myco-compounds (phenolics) with respect to antitumor substances and molecules with modulatory effects on epigenetic events was used. For the screening of mushroom molecules with potential regulatory effects on epigenome (obtained on Web of Science, August 2015), the enzymes histone acetyltransferase (HAT), histone deacetylase (HDAC) and DNA methyltransferase (DNMT) were chosen as targets. Similarity analysis were performed with the software Saranea. Moreover, the determination of the chemical structural similitude between phenolic compounds of Pleurotus ostreatus (oyster mushroom) and antitumor reference compounds was carried out with the software Power MV 0.61. Tanimoto’s coefficients (Tc) similar or higher to 0.90 were considered as significant. Results: Seven mushroom compounds with high structural similarity to reference substances with modulatory activity on epigenetic events (Tc ≥0.90) were identified: 5 with a potential effect on histone acetylation/deacetylation, and 3 acting on the enzyme DNMT. Twenty antitumor reference compounds showed structural similarity to 3 phenols occurring in P. ostreatus, corresponding the largest number to protocatechuic acid and the flavonoids myricetin and naringin. According to its similarity to the antitumor compounds, they would act as DNA antimetabolites, antimitotic, and/or alkylating agents. Conclusion: It seems feasible to harness the natural pool of mushrooms secondary metabolites and to predict by in silico approaches their potential modulatory effects on epigenetic events and antitumor activity, in special phenolics occurring in P. ostreatus. This is an exciting advance for developing nutraceuticals/ cosmeceuticals and innovative drugs.

Synthesis and Profiling of a Novel Potent Selective Inhibitor of CHK1 Kinase Possessing Unusual N-trifluoromethylpyrazole Pharmacophore Resistant to Metabolic N-dealkylation.

Checkpoint-mediated dependency of tumor cells can be deployed to selectively kill them without substantial toxicity to normal cells. Specifically, loss of CHK1, a serine threonine kinase involved in the surveillance of the G2-M checkpoint in the presence of replication stress inflicted by DNA-damaging drugs, has been reported to dramatically influence the viability of tumor cells. CHK1's pivotal role in maintaining genomic stability offers attractive opportunity for increasing the selectivity, effectivity, and reduced toxicity of chemotherapy. Some recently identified CHK1 inhibitors entered clinical trials in combination with DNA antimetabolites. Herein, we report synthesis and profiling of MU380, a nontrivial analogue of clinically profiled compound SCH900776 possessing the highly unusual N-trifluoromethylpyrazole motif, which was envisioned not to undergo metabolic oxidative dealkylation and thereby provide greater robustness to the compound. MU380 is a selective and potent inhibitor of CHK1 which sensitizes a variety of tumor cell lines to hydroxyurea or gemcitabine up to 10 times. MU380 shows extended inhibitory effects in cells, and unlike SCH900776, does not undergo in vivo N-dealkylation to the significantly less selective metabolite. Compared with SCH900776, MU380 in combination with GEM causes higher accumulation of DNA damage in tumor cells and subsequent enhanced cell death, and is more efficacious in the A2780 xenograft mouse model. Overall, MU380 represents a novel state-of-the-art CHK1 inhibitor with high potency, selectivity, and improved metabolic robustness to oxidative N-dealkylation. Mol Cancer Ther; 16(9); 1831-42. ©2017 AACR.

Elevated cyclin A associated kinase activity promotes sensitivity of metastatic human cancer cells to DNA antimetabolite drug.

Drug resistance is a major obstacle in successful systemic therapy of metastatic cancer. We analyzed the involvement of cell cycle regulatory proteins in eliciting response to N (phosphonoacetyl)-L-aspartate (PALA), an inhibitor of de novo pyrimidine synthesis, in two metastatic variants of human cancer cell line MDA-MB-435 isolated from lung (L-2) and brain (Br-1) in nude mouse, respectively. L-2 and Br-l cells markedly differed in their sensitivity to PALA. While both cell types displayed an initial S phase delay/arrest, Br-l cells proliferated but most L-2 cells underwent apoptosis. There was distinct elevation in cyclin A, and phosphorylated Rb proteins concomitant with decreased expression of bcl-2 protein in the PALA treated L-2 cells undergoing apoptosis. Markedly elevated cyclin A associated and cdk2 kinase activities together with increased E2F1-DNA binding were detected in these L-2 cells. Induced ectopic cyclin A expression sensitized Br-l cells to PALA by activating an apoptotic pathway. Our findings demonstrate that elevated expression of cyclin A and associated kinase can activate an apoptotic pathway in cells exposed to DNA antimetabolites. Abrogation of this pathway can lead to resistance against these drugs in metastatic variants of human carcinoma cells.

Targeting the Replication Checkpoint Using SCH 900776, a Potent and Functionally Selective CHK1 Inhibitor Identified via High Content Screening

Checkpoint kinase 1 (CHK1) is an essential serine/threonine kinase that responds to DNA damage and stalled DNA replication. CHK1 is essential for maintenance of replication fork viability during exposure to DNA antimetabolites. In human tumor cell lines, ablation of CHK1 function during antimetabolite exposure led to accumulation of double-strand DNA breaks and cell death. Here, we extend these observations and confirm ablation of CHK2 does not contribute to these phenotypes and may diminish them. Furthermore, concomitant suppression of cyclin-dependent kinase (CDK) activity is sufficient to completely antagonize the desired CHK1 ablation phenotypes. These mechanism-based observations prompted the development of a high-content, cell-based screen for γ-H2AX induction, a surrogate marker for double-strand DNA breaks. This mechanism-based functional approach was used to optimize small molecule inhibitors of CHK1. Specifically, the assay was used to mechanistically define the optimal in-cell profile with compounds exhibiting varying degrees of CHK1, CHK2, and CDK selectivity. Using this approach, SCH 900776 was identified as a highly potent and functionally optimal CHK1 inhibitor with minimal intrinsic antagonistic properties. SCH 900776 exposure phenocopies short interfering RNA-mediated CHK1 ablation and interacts synergistically with DNA antimetabolite agents in vitro and in vivo to selectively induce dsDNA breaks and cell death in tumor cell backgrounds.

Modeling of drug molecule orientation within a receptor cavity in the BiS algorithm framework

The BiS algorithm is suggested for modeling the drug molecule orientation within a receptor cavity. It is based on the assumption of complementarity of the field created by biologically active compounds and the field of the responsive receptor. The comparison of predicted orientations of various biologically active compounds on the relevant receptors with the data of X-ray structural studies (Protein Data Bank) reveals that the results obtained with this approach surpasses those reported in the literature. The suggested technique made it possible to elucidate the details of the action mechanism of DNA antimetabolites, dihydrofolate reductase inhibitors. The dependence of the activity on the structural parameters of “ligand-receptor” complexes is determined.

Structure-based rationalization of antitumor drugs mechanism of action by a MIF approach

Structural patterns for antitumor drugs, evidenced by means of a molecular interaction field (MIF) approach using grid independent descriptors (GRIND), resembled closely those of a previous independent pharmacological classification based on their antitumor mechanism of action. For topoisomerase II inhibitors, antimitotic agents and DNA antimetabolites, systematic structural patterns were evidenced by MIF and the structural features of “outliers” in these classes corresponded to peculiar pharmacological mechanisms of action supported by literature evidences. Alkylating agents and DNA/RNA antimetabolites, interacting with a large variety of targets by different molecular mechanisms, did not exhibit clustering in the structure-based MIF approach. Moreover MIFS were able to point out similarities between drugs which, in spite of apparent dramatic differences in chemical structure, exhibit the same pharmacological behaviour.

Identifying genes related to drug anticancer mechanisms using support vector machine

In an effort to identify genes related to the cell line chemosensitivity and to evaluate the functional relationships between genes and anticancer drugs acting by the same mechanism, a supervised machine learning approach called support vector machine was used to label genes into any of the five predefined anticancer drug mechanistic categories. Among dozens of unequivocally categorized genes, many were known to be causally related to the drug mechanisms. For example, a few genes were found to be involved in the biological process triggered by the drugs (e.g. DNA polymerase epsilon was the direct target for the drugs from DNA antimetabolites category). DNA repair-related genes were found to be enriched for about eight-fold in the resulting gene set relative to the entire gene set. Some uncharacterized transcripts might be of interest in future studies. This method of correlating the drugs and genes provides a strategy for finding novel biologically significant relationships for molecular pharmacology.

Nitric oxide enhancement of fludarabine cytotoxicity for B-CLL lymphocytes.

Fludarabine is active but not curative in the treatment of chronic lymphocytic leukemia (B-CLL). Nitric oxide (NO) supplied from exogenous, NO-donating pro-drugs can also induce apoptosis and death of acute leukemia cells. This study investigated combinations of fludarabine with NO-donating pro-drugs for their cytotoxicity against freshly isolated B-CLL lymphocytes following a 72 h exposure in vitro. The median IC(50)for fludarabine was 2.2 microM (n = 85). The nitric oxide donors DETA-NO, PAPA-NO, and MAHMA-NO were also cytotoxic, and their effects were inversely related to rates of NO release. Neither DETA-NO depleted of NO nor DETA itself was effective, indicating that NO was required for cytotoxicity. Drug interactions were evaluated by a modified combination index method. Synergy was observed in combinations of fludarabine or nelarabine (506U78) with DETA-NO in 52% and 88% of samples, respectively. Interestingly, the combination of fludarabine and DETA-NO was more cytotoxic in B-CLL cells less sensitive to fludarabine. DETA-NO did not enhance the activity of other DNA anti-metabolites, topoisomerase I and II inhibitors, or alkylating agents. Finally, the anti-leukemic activity of fludarabine alone or in combination with DETA-NO was found to correlate with inhibition of cellular RNA synthesis. These results indicate that NO donors could enhance fludarabine therapy for B-CLL.

Induction of virus synthesis in polyoma-transformed cells by DNA antimetabolites and by irradiation after pretreatment with 5-bromodeoxyuridine

Polyoma-virus (PV)-transformed cells which exhibited a spontaneous induction rate of about 1 × 10−4 cells for polyoma viral capsid (V) antigen synthesis, producing 100 plaque-forming units (PFU) per induced cell, were shown to be inducible for PV synthesis by various DNA antimetabolites. Mitomycin C (MC), nitrogen mustard (NH2), and N-nitrosomethylurea (NMU) induced 43, 24, and 9% of cells, respectively, for V antigen synthesis. The yields of infectious virus in the treated cultures were increased by a factor of up to 5 × 102, as compared to untreated cultures. The inducibility of the cells by MC, NH2, and NMU was shown to be dose-dependent increasing with the concentration of the inducing compounds to a maximum which varied for each inducer. Among the induced cells, some did not produce infectious virus, but produced V antigen; in the cultures which exhibited maximum cell inducibility for V antigen synthesis, only about 38–47% of the V antigen-containing cells produced virus. The synthesis of V antigen and of infectious virus was shown to occur in cells irreversibly blocked for cell division by the inducing agents. Bromodeoxyuridine, iododeoxyuridine, and fluorodeoxyuridine induced V antigen production in 0.8–1.4% cells, the induced cells yielding an average of 12–50 PFU per cell. Pretreatment of the cells with bromodeoxyuridine increased the inducibility of the cells for V antigen production by UV and X-irradiation, by factors of up to 10 and 15, respectively, and for infectious virus synthesis by factors of up to 5 and 6, respectively. The results suggest that the cellular DNA is the target for induction of virus synthesis in these cells and that damage of the cellular DNA results in activation of the virus genome.