Identification of potent catalytic inhibitors of human DNA topoisomerase II by structure-based virtual screening

QSAR, molecular docking, and pharmacokinetic analysis of thiosemicarbazone-indole compounds targeting prostate cancer cells

Objectives

By 2030, prostate cancer is estimated to account for 1.7 million new cases and 499,000 deaths. The objectives of this research were to create a model revealing the activity of thiosemicarbazone-indole compounds as anticancer agents against the PC3 cell line; perform docking analysis between the compounds and the target enzyme; and predict the pharmacokinetics and drug-likeness of the compounds under investigation.

Methods

The quantitative structureactivity relationship (QSAR) method was used to build the model; molecular docking between the compounds and the target enzyme was performed; and the drug-likeness and pharmacokinetics of the inhibiting compounds was examined.

Results

The genetic function algorithm-multilinear regression approach was used for building the QSAR model. Build model 1 had the best performance, with R2 (coefficient of determination) = 0.972517, Radj (adjusted R-squared) = 0.964665, (CRp2) = 0.780922, and LOF (leave-one-out cross-validation) = 0.076524, demonstrated strongly indicated by the molecular descriptors. SHBd, SsCH3, JGI2, and RDF60P were highly dependent on proliferative activity. Compounds ID 7 and 22 had the potential to act as androgen receptor inhibitors, as suggested by molecular docking studies between the drugs and their target enzymes. Compounds ID 7 and 22 exhibited binding scores of -8.5 kcal/mol and -8.8 kcal/mol, respectively. The approved maximum medication molecules for oral bioavailability included the molecules with IDs 7 and 22.

Conclusion

This research provides valuable insights into the relationships among molecular descriptors, potential inhibitors, and pharmacokinetic properties in the treatment of PC3. These findings may contribute to the understanding and potential development of new therapeutic options for prostate cancer patients.

The Implication of Topoisomerase II Inhibitors in Synthetic Lethality for Cancer Therapy

DNA topoisomerase II (Top2) is essential for all eukaryotic cells in the regulation of DNA topology through the generation of temporary double-strand breaks. Cancer cells acquire enhanced Top2 functions to cope with the stress generated by transcription and DNA replication during rapid cell division since cancer driver genes such as Myc and EZH2 hijack Top2 in order to realize their oncogenic transcriptomes for cell growth and tumor progression. Inhibitors of Top2 are therefore designed to target Top2 to trap it on DNA, subsequently causing protein-linked DNA breaks, a halt to the cell cycle, and ultimately cell death. Despite the effectiveness of these inhibitors, cancer cells can develop resistance to them, thereby limiting their therapeutic utility. To maximize the therapeutic potential of Top2 inhibitors, combination therapies to co-target Top2 with DNA damage repair (DDR) machinery and oncogenic pathways have been proposed to induce synthetic lethality for more thorough tumor suppression. In this review, we will discuss the mode of action of Top2 inhibitors and their potential applications in cancer treatments.

Determination of anticancer potential of a novel pharmacologically active thiosemicarbazone derivative in colorectal cancer cell lines

Thiosemicarbazones have received noteworthy attention due to their numerous pharmacological activities. Various thiosemicarbazone derivatives have been reported to play a key role as potential chemotherapeutic agents for the management of cancer. Herein, we aimed to establish the anticancer efficacy of novel thiosemicarbazone derivative C4 against colon cancer in vitro. The MTT viability assay identified C4 as a promising anticancer compound in a panel of cancer cell lines with the most potent activity against colon cancer cells. Further, anticancer potential of C4 was evaluated against HT-29 and SW620 colon cancer cell lines considering the factors like cell adhesion and migration, oxidative stress, cell cycle arrest, and apoptosis. Our results showed that C4 significantly inhibited the migration and adhesion of colon cancer cells. C4 significantly increased the intracellular reactive oxygen species (ROS) and induced apoptotic cell death. Cell cycle analysis revealed that C4 interfered in the cell cycle distribution and arrested the cells at the G2/M phase of the cell cycle. Consistent with these results C4 also down-regulated the Bcl-XL and Bcl-2 and up-regulated the caspase-3 expression. These findings introduced C4 as the potential anticancer agent against colon cancer.

Smoothed Potential MD Simulations for Dissociation Kinetics of Etoposide To Unravel Isoform Specificity in Targeting Human Topoisomerase II

Human type II topoisomerases (TopoII) are essential for controlling DNA topology within the cell. For this reason, there are a number of TopoII-targeted anticancer drugs that act by inducing DNA cleavage mediated by both TopoII isoforms (TopoIIα and TopoIIβ) in cells. However, recent studies suggest that specific poisoning of TopoIIα may be a safer strategy for treating cancer. This is because poisoning of TopoIIβ appears to be linked to the generation of secondary leukemia in patients. We recently reported that enzyme-mediated DNA cleavage complexes (in which TopoII is covalently linked to the cleaved DNA during catalysis) formed in the presence of the anticancer drug etoposide persisted approximately 3-fold longer with TopoIIα than TopoIIβ. Notably, enhanced drug-target residence time may reduce the adverse effects of specific TopoIIα poisons. However, it is still not clear how to design drugs that are specific for the α isoform. In this study, we report the results of classical molecular dynamics (MD) simulations to comparatively analyze the molecular interactions formed within the TopoII/DNA/etoposide complex with both isoforms. We also used smoothed potential MD to estimate etoposide dissociation kinetics from the two isoform complexes. These extensive classical and enhanced sampling simulations revealed stabilizing interactions of etoposide with two serine residues (Ser763 and Ser800) in TopoIIα. These interactions are missing in TopoIIβ, where both amino acids are alanine residues. This may explain the greater persistence of etoposide-stabilized cleavage complexes formed with Topo TopoIIα. These findings could be useful for the rational design of specific TopoIIα poisons.

Computational studies, design and synthesis of Pd(II)-based complexes: Allosteric inhibitors of the Human Topoisomerase-IIα

Herein, a robust docking protocol was developed by using a low-cost workflow to highlight the modulation at ATPase domain from Human Topoisomerase-IIα (TOP2A) towards four novel Pd(II)-complexes bearing N,S-donor ligands. In vitro TOP2A inhibition assay confirmed the ability of them to prevent the enzyme functions into concentration ranging at 6.25-25μM. These results exhibited more effectivity than anticancer agent etoposide (35μM) and merbarone (40-50μM). The compounds were screened via Resazurin assay against MCF-7, MDA-MB-231 (Human breast), DU-145 (Human prostate), A549 (Human lung) and Cal27 (Human tongue) tumor cell lines revealing great cytotoxic effects, primarily to MCF-7 (IC₅₀=1.81-4.46μM). As well, 1-4 exhibited their selectivity index (SI) higher than cisplatin against HEK-293 (human kidney) normal cells, at least 11.6-fold (SI_1-4=1.4-5.0; SI_cis=0.12). Further, Red Blood Cell hemolytic test suggested in vitro non-toxic character for compound 4, previously evaluated as the most effective TOP2A inhibitor.

Synthesis and antitumor activity of 2-isocamphanyl thiosemicarbazone derivatives via ROS-enhanced mitochondrial damage

A series of novel 2-isocamphanyl thiosemicarbazone derivatives were synthesized and characterized by ¹ H NMR, ¹³ C NMR, and HRMS. In in vitro anticancer activity, most derivatives showed considerable cytotoxic activity against four cancer cell lines (RPMI-8226, A549, MDA-MB-231, and HepG2 cancer cells) and showed low toxicity against human gastric mucosal cells (GES-1). Among them, compound 4h exhibited excellent antitumor activity against the tested cancer cells with IC₅₀ values of 0.4, 1.1, 1.6, and 1.7 μM for MDA-MB-231, RPMI-8226, A549, and HepG2, respectively. Further, mechanism studies indicated that compound 4h induced apoptosis in MDA-MB-231 cells through enhancing reactive oxygen species levels, inducing mitochondrial membrane potential decrease, and influencing the expression of Bax, Bcl-2, caspase-3, and caspase-9.

The compromise of virtual screening and its impact on drug discovery

Introduction: Docking and structure-based virtual screening (VS) have been standard approaches in structure-based design for over two decades. However, our understanding of the limitations, potential, and strength of these techniques has enhanced, raising expectations. Areas covered: Based on a survey of reports in the past five years, we assess whether VS: (1) predicts binding poses in agreement with crystallographic data (when available); (2) is a superior screening tool, as often claimed; (3) is successful in identifying chemical scaffolds that can be starting points for subsequent lead optimization cycles. Data shows that knowledge of the target and its chemotypes in postprocessing lead to viable hits in early drug discovery endeavors. Expert opinion: VS is capable of accurate placements in the pocket for the most part, but does not consistently score screening collections accurately. What matters is capitalization on available resources to get closer to a viable lead or optimizable series. Integration of approaches, subjective hit selection guided by knowledge of the receptor or endogenous ligand, libraries driven by experimental guides, validation studies to identify the best docking/scoring that reproduces experimental findings, constraints regarding receptor-ligand interactions, thoroughly designed methodologies, and predefined cutoff scoring criteria strengthen VS's position in pharmaceutical research.