Molecular Classification of Antitubulin Agents with Indole Ring Binding at Colchicine-Binding Site

Background: The role of microtubules in cell division and signaling, intercellular transport, and mitosis has been well known. Hence, they have been targeted for several anti-cancer drugs. Methods: A series of 3-(alkylthio)-5,6-diphenyl-1,2,4-triazines were prepared and evaluated for their cytotoxic activities in vitro against three human cancer cell lines; human colon carcinoma cells HT-29, human breast adenocarcinoma cell line MCF-7, human Caucasian gastric adenocarcinoma cell line AGS as well as fibroblast cell line NIH-3T3 by MTT assay. Docking simulation was performed to insert these compounds into the crystal structure of tubulin at the colchicine binding site to determine a probable binding model. Compound 5d as the most active compound was selected for studying of microtubule disruption. Results: Compound 5d showed potent cytotoxic activity against all cell lines. The molecular modeling study revealed that some derivatives of triazine strongly bind to colchicine binding site. The tubulin polymerization assay kit showed that the cytotoxic activity of 5d may be related to inhibition of tubulin polymerization. Conclusion: The cytotoxicity and molecular modeling study of the synthesized compounds with their inhibition activity in tubulin polymerization demonstrate the potential of triazine derivatives for development of new anti-cancer agents.

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Synthesis and tubulin interaction of thiocolchicines containing an isothiocyanato group. Synthesis of C(2)-deuterated and C(2)-14C-labeled 7-isothiocyanatodeacetamidothiocolchicine

Collection of Czechoslovak Chemical Communications ◽

10.1135/cccc19912306 ◽

1991 ◽

Vol 56 (11) ◽

pp. 2306-2312 ◽

Cited By ~ 3

Author(s):

Anjum Muzaffar ◽

Ernest Hamel ◽

Rouli Bai ◽

Arnold Brossi

Keyword(s):

Binding Site ◽

Covalent Bond ◽

Tubulin Polymerization ◽

Low Concentration ◽

Covalent Interaction ◽

Isotope Label ◽

Colchicine Binding Site

Synthesis of isothiocyanato substituted thiocolchicines XI - XIV is described. Introduction of an isotope label is demonstrated with the deuterated isothiocyanate XII and the 14C-labeled analog XIII. These isothiocyanates inhibit tubulin polymerization at low concentration. In addition, the 14C-labeled XIII forms covalent bond(s) with tubulin. Unfortunately, the covalent reaction while rapid, is not inhibited by preincubation of tubulin with colchicine. The covalent interaction of XIII with tubulin thus appears to be nonspecific, limiting its use as a marker of the colchicine binding site on tubulin.

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Normal tissue content impact on the GBM molecular classification

Briefings in Bioinformatics ◽

10.1093/bib/bbaa129 ◽

2020 ◽

Author(s):

Rodrigo Madurga ◽

Noemí García-Romero ◽

Beatriz Jiménez ◽

Ana Collazo ◽

Francisco Pérez-Rodríguez ◽

...

Keyword(s):

Normal Tissue ◽

In Silico Analysis ◽

Molecular Classification ◽

Gene Signature ◽

Normal Brain ◽

Normal Cells ◽

Final Model ◽

Tumor Subtypes ◽

Tissue Content

Abstract Molecular classification of glioblastoma has enabled a deeper understanding of the disease. The four-subtype model (including Proneural, Classical, Mesenchymal and Neural) has been replaced by a model that discards the Neural subtype, found to be associated with samples with a high content of normal tissue. These samples can be misclassified preventing biological and clinical insights into the different tumor subtypes from coming to light. In this work, we present a model that tackles both the molecular classification of samples and discrimination of those with a high content of normal cells. We performed a transcriptomic in silico analysis on glioblastoma (GBM) samples (n = 810) and tested different criteria to optimize the number of genes needed for molecular classification. We used gene expression of normal brain samples (n = 555) to design an additional gene signature to detect samples with a high normal tissue content. Microdissection samples of different structures within GBM (n = 122) have been used to validate the final model. Finally, the model was tested in a cohort of 43 patients and confirmed by histology. Based on the expression of 20 genes, our model is able to discriminate samples with a high content of normal tissue and to classify the remaining ones. We have shown that taking into consideration normal cells can prevent errors in the classification and the subsequent misinterpretation of the results. Moreover, considering only samples with a low content of normal cells, we found an association between the complexity of the samples and survival for the three molecular subtypes.

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Molecular Classification and Tumor Microenvironment Characterization of Gallbladder Cancer by Comprehensive Genomic and Transcriptomic Analysis

Cancers ◽

10.3390/cancers13040733 ◽

2021 ◽

Vol 13 (4) ◽

pp. 733

Author(s):

Nobutaka Ebata ◽

Masashi Fujita ◽

Shota Sasagawa ◽

Kazuhiro Maejima ◽

Yuki Okawa ◽

...

Keyword(s):

Tumor Microenvironment ◽

Gallbladder Cancer ◽

Epithelial To Mesenchymal Transition ◽

Molecular Classification ◽

Mesenchymal Transition ◽

Elevated Expression ◽

Fresh Frozen ◽

Therapeutic Decision Making

Gallbladder cancer (GBC), a rare but lethal disease, is often diagnosed at advanced stages. So far, molecular characterization of GBC is insufficient, and a comprehensive molecular portrait is warranted to uncover new targets and classify GBC. We performed a transcriptome analysis of both coding and non-coding RNAs from 36 GBC fresh-frozen samples. The results were integrated with those of comprehensive mutation profiling based on whole-genome or exome sequencing. The clustering analysis of RNA-seq data facilitated the classification of GBCs into two subclasses, characterized by high or low expression levels of TME (tumor microenvironment) genes. A correlation was observed between gene expression and pathological immunostaining. TME-rich tumors showed significantly poor prognosis and higher recurrence rate than TME-poor tumors. TME-rich tumors showed overexpression of genes involved in epithelial-to-mesenchymal transition (EMT) and inflammation or immune suppression, which was validated by immunostaining. One non-coding RNA, miR125B1, exhibited elevated expression in stroma-rich tumors, and miR125B1 knockout in GBC cell lines decreased its invasion ability and altered the EMT pathway. Mutation profiles revealed TP53 (47%) as the most commonly mutated gene, followed by ELF3 (13%) and ARID1A (11%). Mutations of ARID1A, ERBB3, and the genes related to the TGF-β signaling pathway were enriched in TME-rich tumors. This comprehensive analysis demonstrated that TME, EMT, and TGF-β pathway alterations are the main drivers of GBC and provides a new classification of GBCs that may be useful for therapeutic decision-making.

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Structural insights into targeting of the colchicine binding site by ELR510444 and parbendazole to achieve rational drug design

RSC Advances ◽

10.1039/d1ra01173a ◽

2021 ◽

Vol 11 (31) ◽

pp. 18938-18944

Author(s):

Jia-Hong Lei ◽

Ling-Ling Ma ◽

Jing-Hong Xian ◽

Hai Chen ◽

Jian-Jian Zhou ◽

...

Keyword(s):

Drug Design ◽

Binding Site ◽

Crystal Structures ◽

Rational Drug Design ◽

Colchicine Binding Site ◽

Rational Drug ◽

Structural Insights

Crystal structures of tubulin complexed with ELR510444 and parbendazole facilitate the design of novel colchicine binding site inhibitors.

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A photoaffinity derivative of colchicine: 6'-(4'-azido-2'-nitrophenylamino)hexanoyldeacetylcolchicine. Photolabeling and location of the colchicine-binding site on the alpha-subunit of tubulin.

Journal of Biological Chemistry ◽

10.1016/s0021-9258(17)38795-1 ◽

1985 ◽

Vol 260 (25) ◽

pp. 13794-13802

Author(s):

R F Williams ◽

C L Mumford ◽

G A Williams ◽

L J Floyd ◽

M J Aivaliotis ◽

...

Keyword(s):

Binding Site ◽

Alpha Subunit ◽

Colchicine Binding Site

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