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Journal of Tropical Medicine 2024is a therapeutic plant traditionally used to treat rabies, snake bite, diarrhea, and wound healing. To address the bioactive compounds exhibiting these activities, we...
is a therapeutic plant traditionally used to treat rabies, snake bite, diarrhea, and wound healing. To address the bioactive compounds exhibiting these activities, we performed a comprehensive study on the roots of the plant. Thus, the present study aims to inspect the antioxidant and antibacterial efficacies of compounds isolated from the combined dichloromethane : methanol (1 : 1) and methanol extracts of along with the study of their interaction with selected protein targets. The silica gel column chromatography technique was used for the isolation of compounds, and the antibacterial and antioxidant activities were evaluated using agar disc diffusion and DPPH radical scavenging assays, respectively. Furthermore, molecular docking screening, pharmacokinetics, and toxicity protocols of the compound isolates were performed to offer the potential applications of the compounds in developing novel medications. A BIOVIA Discovery Studio in combination with AutoDock Vina 4.2 software, SwissADME, and ProTox-II prediction web tools were used to generate the molecular docking, pharmacokinetics, and toxicity profiles, respectively. Notably, the chromatographic separation of the combined extracts yielded six known compounds, namely, sitosterol (), 3-hydroxyisoagatholactone (), -viniferin (), myricetin (), tricuspidatol A (), and parthenocissin A (). The antibacterial activities revealed the highest inhibition zone by tricuspidatol A () (16.67 ± 0.47), showcasing its potent activity against at 2 mg/mL, compared to ciprofloxacin (21.50 ± 0.41). -Viniferin () (IC: 0.32 g/mL) exhibited greater antioxidant activity than the others and displayed promising results compared to ascorbic acid (0.075 g/mL). The molecular docking study revealed the highest binding affinity by viniferin () (-9.9 kcal/mol) against topoisomerase II 3-Hydroxyisoagatholactone () and -viniferin () fulfilled Lipinski's rule with no violation, and the organ toxicity predictions revealed that all the compounds showed no cytotoxicity and hepatotoxicity effects. Thus, this study's combined and outcomes suggest the potential use of the isolated compounds in drug discovery and support the traditional relevance of .
PubMed: 38482509
DOI: 10.1155/2024/1679695 -
Translational Cancer Research Feb 2024Hepatitis B virus (HBV) is the dominant pathogenic factor of hepatocellular carcinoma (HCC) in Asia and Africa. Early identification and clinical diagnosis are crucial...
BACKGROUND
Hepatitis B virus (HBV) is the dominant pathogenic factor of hepatocellular carcinoma (HCC) in Asia and Africa. Early identification and clinical diagnosis are crucial for HBV-related HCC. Random forest (RF) and artificial neural network (ANN) were an innovative and highly effective supervised machine learning (ML) algorithm for the early diagnosis and screening of HBV-related HCC. This study aims to identify significant biomarkers and develop a novel genetic model for the efficient diagnosis of HBV-related HCC.
METHODS
Gene Expression Omnibus (GEO) Series (GSE)19665, GSE55092, and GSE121248 were used to identify significant differentially expressed genes (DEGs). The enrichment analysis was performed on Metascape online tool. The RF algorithm and ANN were used to select the potential predictive gene panels and construct an HBV-related HCC diagnostic model. Subsequently, GSE17548, GSE104310, GSE44074, and GSE136247 were used to test the accuracy of the ANN model. Finally, the CIBERSORT algorithm was used to assess the abundance of immune infiltrates in all samples.
RESULTS
First, 116 genes were identified as DEGs, and the DEGs were particularly enriched in cellular hormone metabolic process, monocarboxylic acid metabolic process, NABA extracellular matrix (ECM) AFFILIATED steroid metabolic process and metabolism of bile acid and bile salt. DNA topoisomerase II alpha (), C-type lectin domain family 1 member B (), BUB1 mitotic checkpoint serine/threonine kinase B (), ficolin 2 (), C-X-C motif chemokine ligand 14 (), cyclase associated actin cytoskeleton regulatory protein 2 (), ficolin 3 (), kynurenine 3-monooxygenase () and cadherin related family member 2 () were available to develop an HBV-related HCC diagnostic model. After validation, the diagnostic model showed high sensitivity (88.5%, 90%, 88.5%, 76.5%) and specificity (100%, 81.8%, 89.5%, 72.2%), and the areas under the receiver operating characteristic (ROC) curves showed excellent efficiency (1, 0.927, 0.921, 0.833). Finally, the percentage of infiltrating immune cell types [B cells naïve, B cells memory, plasma cells, T cells CD8, T cells CD4 memory resting, T cells regulatory (Tregs), T cells gamma delta, natural killer (NK) cells resting, NK cells activated, Macrophages M0, Dendritic cells activated, Mast cells activated] for hepatitis B-related HCC were significantly different from that of non-cancerous liver tissue with HBV.
CONCLUSIONS
A novel early diagnostic model of HBV-related HCC was established, and the model showed better efficiency in distinguishing HBV-related HCC from other non-cancerous with HBV individuals.
PubMed: 38482416
DOI: 10.21037/tcr-23-1197 -
International Journal of Molecular... Feb 2024New amide conjugates of hydroxycinnamic acids (HCAs) and the known antineoplastic 5,11-dimethyl-5-indolo[2,3-]quinoline (DiMIQ), an analog of the natural alkaloid...
New amide conjugates of hydroxycinnamic acids (HCAs) and the known antineoplastic 5,11-dimethyl-5-indolo[2,3-]quinoline (DiMIQ), an analog of the natural alkaloid neocryptolepine, were synthesized and tested in vitro for anticancer activity. The compound 9-[((2-hydroxy)cinnamoyl)amino]-5,11-dimethyl-5-indolo[2,3-]quinoline (), which contains the ortho-coumaric acid fragment, demonstrated dose-dependent effectiveness against both normal BxPC-3 and metastatic AsPC-1 pancreatic cancer cells. The IC values for AsPC-1 and BxPC-3 were 336.5 nM and 347.5 nM, respectively, with a selectivity index of approximately 5 for both pancreatic cancer cells compared to normal dermal fibroblasts. Conjugate did not exhibit any hemolytic activity against human erythrocytes at the tested concentration. Computational studies were performed to predict the pharmacokinetic profile and potential mechanism of action of the synthesized conjugates. These studies focused on the ADME properties of the conjugates and their interactions with DNA, as well as DNA-topoisomerase alpha and beta complexes. All of the conjugates studied showed approximately one order of magnitude stronger binding to DNA compared to the reference DiMIQ, and approximately two orders of magnitude stronger binding to the topoisomerase II-DNA complex compared to DiMIQ. Conjugate was predicted to have the strongest binding to the enzyme-DNA complex, with a Ki value of 2.8 nM.
Topics: Humans; Molecular Docking Simulation; Pancreatic Hormones; Pancreatic Neoplasms; Quinolines; Antineoplastic Agents; Coumaric Acids; Multienzyme Complexes; DNA; Structure-Activity Relationship; Molecular Structure; Cell Line, Tumor
PubMed: 38473820
DOI: 10.3390/ijms25052573 -
Breast Cancer Research and Treatment Jun 2024Previous studies have reported the benefit of dual HER2-targeting combined to neoadjuvant chemotherapy in HER2-amplified breast cancer (HER2 + BC). Moreover, besides...
Neoadjuvant anthracycline-based (5-FEC) or anthracycline-free (docetaxel/carboplatin) chemotherapy plus trastuzumab and pertuzmab in HER2 + BC patients according to their TOP2A: a multicentre, open-label, non-randomized phase II trial.
PURPOSE
Previous studies have reported the benefit of dual HER2-targeting combined to neoadjuvant chemotherapy in HER2-amplified breast cancer (HER2 + BC). Moreover, besides the cardiac toxicity following their association to Trastuzumab, anthracyclines chemotherapy may not profit all patients. The NeoTOP study was designed to evaluate the complementary action of Trastuzumab and Pertuzumab, and the relevance of an anthracycline-based regimen according to TOP2A amplification status.
METHODS
Open-label, multicentre, phase II study. Eligible patients were aged ≥ 18 with untreated, operable, histologically confirmed HER2 + BC. After centralized review of TOP2A status, TOP2A-amplified (TOP2A+) patients received FEC100 for 3 cycles then 3 cycles of Trastuzumab (8 mg/kg then 6 mg/kg), Pertuzumab (840 mg/kg then 420 mg/kg), and Docetaxel (75mg/m then 100mg/m). TOP2A-not amplified (TOP2A-) patients received 6 cycles of Docetaxel (75mg/m) and Carboplatin (target AUC 6 mg/ml/min) plus Trastuzumab and Pertuzumab. Primary endpoint was pathological Complete Response (pCR) using Chevallier's classification. Secondary endpoints included pCR (Sataloff), Progression-Free Survival (PFS), Overall Survival (OS), and toxicity.
RESULTS
Out of 74 patients, 41 and 33 were allocated to the TOP2A + and TOP2A- groups respectively. pCR rates (Chevallier) were 74.4% (95%CI: 58.9-85.4) vs. 71.9% (95%CI: 54.6-84.4) in the TOP2A + vs. TOP2A- groups. pCR rates (Sataloff), 5-year PFS and OS were 70.6% (95%CI: 53.8-83.2) vs. 61.5% (95%CI: 42.5-77.6), 82.4% (95%CI: 62.2-93.6) vs. 100% (95%CI: 74.1-100), and 90% (95%CI: 69.8-98.3) vs. 100% (95%CI: 74.1-100). Toxicity profile was consistent with previous reports.
CONCLUSION
Our results showed high pCR rates with Trastuzumab and Pertuzumab associated to chemotherapy. They were similar in TOP2A + and TOP2A- groups and the current role of neoadjuvant anthracycline-based chemotherapy remains questioned.
TRIAL REGISTRATION NUMBER
NCT02339532 (registered on 14/12/14).
Topics: Humans; Female; Antineoplastic Combined Chemotherapy Protocols; Middle Aged; Trastuzumab; Breast Neoplasms; Neoadjuvant Therapy; Receptor, ErbB-2; Adult; DNA Topoisomerases, Type II; Docetaxel; Carboplatin; Aged; Antibodies, Monoclonal, Humanized; Cyclophosphamide; Fluorouracil; Poly-ADP-Ribose Binding Proteins; Anthracyclines; Epirubicin
PubMed: 38453781
DOI: 10.1007/s10549-024-07285-y -
Nucleic Acids Research Apr 2024CCCTC-binding factor (CTCF) binding sites are hotspots of genome instability. Although many factors have been associated with CTCF binding site fragility, no study has...
CCCTC-binding factor (CTCF) binding sites are hotspots of genome instability. Although many factors have been associated with CTCF binding site fragility, no study has integrated all fragility-related factors to understand the mechanism(s) of how they work together. Using an unbiased, genome-wide approach, we found that DNA double-strand breaks (DSBs) are enriched at strong, but not weak, CTCF binding sites in five human cell types. Energetically favorable alternative DNA secondary structures underlie strong CTCF binding sites. These structures coincided with the location of topoisomerase II (TOP2) cleavage complex, suggesting that DNA secondary structure acts as a recognition sequence for TOP2 binding and cleavage at CTCF binding sites. Furthermore, CTCF knockdown significantly increased DSBs at strong CTCF binding sites and at CTCF sites that are located at topologically associated domain (TAD) boundaries. TAD boundary-associated CTCF sites that lost CTCF upon knockdown displayed increased DSBs when compared to the gained sites, and those lost sites are overrepresented with G-quadruplexes, suggesting that the structures act as boundary insulators in the absence of CTCF, and contribute to increased DSBs. These results model how alternative DNA secondary structures facilitate recruitment of TOP2 to CTCF binding sites, providing mechanistic insight into DNA fragility at CTCF binding sites.
Topics: DNA Topoisomerases, Type II; Humans; CCCTC-Binding Factor; DNA Breaks, Double-Stranded; Binding Sites; DNA; Nucleic Acid Conformation; Protein Binding; Poly-ADP-Ribose Binding Proteins; Cell Line
PubMed: 38452213
DOI: 10.1093/nar/gkae164 -
The Journal of Clinical Investigation Mar 2024Development of effective strategies to manage the inevitable acquired resistance to osimertinib, a third-generation EGFR inhibitor for the treatment of EGFR-mutant...
Development of effective strategies to manage the inevitable acquired resistance to osimertinib, a third-generation EGFR inhibitor for the treatment of EGFR-mutant (EGFRm) non-small cell lung cancer (NSCLC), is urgently needed. This study reports that DNA topoisomerase II (Topo II) inhibitors, doxorubicin and etoposide, synergistically decreased cell survival, with enhanced induction of DNA damage and apoptosis in osimertinib-resistant cells; suppressed the growth of osimertinib-resistant tumors; and delayed the emergence of osimertinib-acquired resistance. Mechanistically, osimertinib decreased Topo IIα levels in EGFRm NSCLC cells by facilitating FBXW7-mediated proteasomal degradation, resulting in induction of DNA damage; these effects were lost in osimertinib-resistant cell lines that possess elevated levels of Topo IIα. Increased Topo IIα levels were also detected in the majority of tissue samples from patients with NSCLC after relapse from EGFR tyrosine kinase inhibitor treatment. Enforced expression of an ectopic TOP2A gene in sensitive EGFRm NSCLC cells conferred resistance to osimertinib, whereas knockdown of TOP2A in osimertinib-resistant cell lines restored their susceptibility to osimertinib-induced DNA damage and apoptosis. Together, these results reveal an essential role of Topo IIα inhibition in mediating the therapeutic efficacy of osimertinib against EGFRm NSCLC, providing scientific rationale for targeting Topo II to manage acquired resistance to osimertinib.
Topics: Humans; Acrylamides; Carcinoma, Non-Small-Cell Lung; Aniline Compounds; ErbB Receptors; Lung Neoplasms; DNA Topoisomerases, Type II; Cell Line, Tumor; Topoisomerase II Inhibitors; Drug Resistance, Neoplasm; Animals; Mice; Mutation; Poly-ADP-Ribose Binding Proteins; Drug Synergism; DNA Damage; Piperazines; Etoposide; Xenograft Model Antitumor Assays
PubMed: 38451729
DOI: 10.1172/JCI172716 -
British Journal of Cancer May 2024Paired related-homeobox 1 (PRRX1) is a transcription factor in the regulation of developmental morphogenetic processes. There is growing evidence that PRRX1 is highly...
BACKGROUND
Paired related-homeobox 1 (PRRX1) is a transcription factor in the regulation of developmental morphogenetic processes. There is growing evidence that PRRX1 is highly expressed in certain cancers and is critically involved in human survival prognosis. However, the molecular mechanism of PRRX1 in cancer malignancy remains to be elucidated.
METHODS
PRRX1 expression in human Malignant peripheral nerve sheath tumours (MPNSTs) samples was detected immunohistochemically to evaluate survival prognosis. MPNST models with PRRX1 gene knockdown or overexpression were constructed in vitro and the phenotype of MPNST cells was evaluated. Bioinformatics analysis combined with co-immunoprecipitation, mass spectrometry, RNA-seq and structural prediction were used to identify proteins interacting with PRRX1.
RESULTS
High expression of PRRX1 was associated with a poor prognosis for MPNST. PRRX1 knockdown suppressed the tumorigenic potential. PRRX1 overexpressed in MPNSTs directly interacts with topoisomerase 2 A (TOP2A) to cooperatively promote epithelial-mesenchymal transition and increase expression of tumour malignancy-related gene sets including mTORC1, KRAS and SRC signalling pathways. Etoposide, a TOP2A inhibitor used in the treatment of MPNST, may exhibit one of its anticancer effects by inhibiting the PRRX1-TOP2A interaction.
CONCLUSION
Targeting the PRRX1-TOP2A interaction in malignant tumours with high PRRX1 expression might provide a novel tumour-selective therapeutic strategy.
Topics: Humans; Homeodomain Proteins; Epithelial-Mesenchymal Transition; DNA Topoisomerases, Type II; Prognosis; Poly-ADP-Ribose Binding Proteins; Cell Line, Tumor; Gene Expression Regulation, Neoplastic; Mice; Animals; Nerve Sheath Neoplasms; Signal Transduction
PubMed: 38448751
DOI: 10.1038/s41416-024-02632-8 -
Cancer Biology & Therapy Dec 2024Ovarian cancer (OC) is a form of gynecological malignancy that is associated with worse patient outcomes than any other cancer of the female reproductive tract....
Ovarian cancer (OC) is a form of gynecological malignancy that is associated with worse patient outcomes than any other cancer of the female reproductive tract. Topoisomerase II α (TOP2A) is commonly regarded as an oncogene that is associated with malignant disease progression in a variety of cancers, its mechanistic functions in OC have yet to be firmly established. We explored the role of TOP2A in OC through online databases, clinical samples, in vitro and in vivo experiments. And initial analyses of public databases revealed high OC-related TOP2A expression in patient samples that was related to poorer prognosis. This was confirmed by clinical samples in which TOP2A expression was elevated in OC relative to healthy tissue. Kaplan-Meier analyses further suggested that higher TOP2A expression levels were correlated with worse prognosis in OC patients. In vitro, TOP2A knockdown resulted in the inhibition of OC cell proliferation, with cells entering G1 phase arrest and undergoing consequent apoptotic death. In rescue assays, TOP2A was confirmed to regulate cell proliferation and cell cycle through AKT/mTOR pathway activity. Mouse model experiments further affirmed the key role that TOP2A plays as a driver of OC cell proliferation. These data provide strong evidence supporting TOP2A as an oncogenic mediator and prognostic biomarker related to OC progression and poor outcomes. At the mechanistic level, TOP2A can control tumor cell growth via AKT/mTOR pathway modulation. These preliminary results provide a foundation for future research seeking to explore the utility of TOP2A inhibitor-based combination treatment regimens in platinum-resistant recurrent OC patients.
Topics: Animals; Female; Humans; Mice; Carcinoma, Ovarian Epithelial; Cell Proliferation; DNA Topoisomerases, Type II; Ovarian Neoplasms; Proto-Oncogene Proteins c-akt; TOR Serine-Threonine Kinases
PubMed: 38445610
DOI: 10.1080/15384047.2024.2325126 -
PLoS Genetics Feb 2024TOP2 inhibitors (TOP2i) are effective drugs for breast cancer treatment. However, they can cause cardiotoxicity in some women. The most widely used TOP2i include...
TOP2 inhibitors (TOP2i) are effective drugs for breast cancer treatment. However, they can cause cardiotoxicity in some women. The most widely used TOP2i include anthracyclines (AC) Doxorubicin (DOX), Daunorubicin (DNR), Epirubicin (EPI), and the anthraquinone Mitoxantrone (MTX). It is unclear whether women would experience the same adverse effects from all drugs in this class, or if specific drugs would be preferable for certain individuals based on their cardiotoxicity risk profile. To investigate this, we studied the effects of treatment of DOX, DNR, EPI, MTX, and an unrelated monoclonal antibody Trastuzumab (TRZ) on iPSC-derived cardiomyocytes (iPSC-CMs) from six healthy females. All TOP2i induce cell death at concentrations observed in cancer patient serum, while TRZ does not. A sub-lethal dose of all TOP2i induces limited cellular stress but affects calcium handling, a function critical for cardiomyocyte contraction. TOP2i induce thousands of gene expression changes over time, giving rise to four distinct gene expression response signatures, denoted as TOP2i early-acute, early-sustained, and late response genes, and non-response genes. There is no drug- or AC-specific signature. TOP2i early response genes are enriched in chromatin regulators, which mediate AC sensitivity across breast cancer patients. However, there is increased transcriptional variability between individuals following AC treatments. To investigate potential genetic effects on response variability, we first identified a reported set of expression quantitative trait loci (eQTLs) uncovered following DOX treatment in iPSC-CMs. Indeed, DOX response eQTLs are enriched in genes that respond to all TOP2i. Next, we identified 38 genes in loci associated with AC toxicity by GWAS or TWAS. Two thirds of the genes that respond to at least one TOP2i, respond to all ACs with the same direction of effect. Our data demonstrate that TOP2i induce thousands of shared gene expression changes in cardiomyocytes, including genes near SNPs associated with inter-individual variation in response to DOX treatment and AC-induced cardiotoxicity.
Topics: Humans; Female; Anthracyclines; Cardiotoxicity; Antibiotics, Antineoplastic; Topoisomerase II Inhibitors; Doxorubicin; Mitoxantrone; Myocytes, Cardiac; Daunorubicin; Epirubicin; DNA Topoisomerases, Type II; Gene Expression
PubMed: 38416769
DOI: 10.1371/journal.pgen.1011164 -
MBio Apr 2024Type II topoisomerase utilizes the energy from ATP hydrolysis to alter DNA topology during genome replication and transcription. The ATPase domain of this enzyme is...
UNLABELLED
Type II topoisomerase utilizes the energy from ATP hydrolysis to alter DNA topology during genome replication and transcription. The ATPase domain of this enzyme is required for ATP hydrolysis and plays a crucial role in coupling DNA binding and ATP turnover with the DNA strand passage reaction. The African swine fever virus (ASFV) specifically encodes a topoisomerase II (topo II), which is critical for viral replication and an attractive target for antiviral development. Here, we present a high-resolution crystal structure of the ASFV topo II ATPase domain complexed with the substrate analog AMPPNP. Structural comparison reveals that the ASFV topo II ATPase domain shares a conserved overall structure with its homologs from eukaryotes and prokaryotes but also has three characteristic regions, including the intra-molecular interface formed by the ATP-lid and QTK loop as well as helix α9, the K-loop in the transducer domain, and the antennae-like α-helix at the ATP binding domain. Mutating the key residues within these three regions impairs or abolishes the basal and DNA-stimulated ATPase activities and reduces or eliminates the relaxation activity of the holoenzyme. Our data indicate that all three regions are functionally important for the ATPase and relaxation activities and strongly suggest that ATP hydrolysis, DNA binding, and strand passage are highly coupled and managed by the allosteric coordination of multiple domains of the type II topoisomerase. Moreover, we find a promising druggable pocket in the dimeric interface of the ASFV topo II ATPase domain, which will benefit future anti-ASFV drug development.
IMPORTANCE
The ATPase domain of type II topoisomerase provides energy by hydrolyzing ATP and coordinates with the DNA-binding/cleavage domain to drive and control DNA transport. The precise molecular mechanisms of how these domains respond to DNA binding and ATP hydrolysis signals and communicate with each other remain elusive. We determine the first high-resolution crystal structure of the ATPase domain of African swine fever virus (ASFV) topo II in complex with AMPPNP and biochemically investigate its function in ATPase and DNA relaxation activities. Importantly, we find that mutations at three characteristic regions of the ASFV ATPase domain produce parallel effects on the basal/DNA-stimulated ATPase and relaxation activities, implying the tight coupling of the ATP hydrolysis and strand passage process. Therefore, our data provide important implications for understanding the strand passage mechanism of the type II topoisomerase and the structural basis for developing ATPase domain-targeting antivirals against ASFV.
Topics: Swine; Animals; African Swine Fever Virus; Adenylyl Imidodiphosphate; DNA Topoisomerases, Type II; DNA; Adenosine Triphosphatases
PubMed: 38411066
DOI: 10.1128/mbio.03086-23