scholarly journals Computational Prediction and Experimental Validation of the Unique Molecular Mode of Action of Scoulerine

2021 ◽  
Author(s):  
M. Moshari ◽  
Q. Wang ◽  
M. Michalak ◽  
M. Klobukowski ◽  
J. A. Tuszynski
Keyword(s):  
Binding Site ◽  
Mode Of Action ◽  
Experimental Validation ◽  
Computational Prediction ◽  
Data Bank ◽  
Microtubule Stabilization ◽  
Colchicine Binding Site ◽  
Molecular Mode ◽  
Similar Affinity ◽  
Computational Predictions

Abstract Scoulerine is a natural compound that is known to bind to tubulin and has anti-mitotic properties demonstrated in various cancer cells. Its molecular mode of action has not been precisely known. In this work we perform computational prediction and experimental validation of the mode of action of scoulerine. Based on the existing data in the Protein Data Bank (PDB) and using homology modeling we create human tubulin structures corresponding to both free tubulin dimers and tubulin in a microtubule. We then perform docking of the optimized structure of scoulerine and find the highest affinity binding sites located in both the free tubulin and in a microtubule. We conclude that binding in the vicinity of the colchicine binding site and near the laulimalide binding site are the most likely locations for scoulerine interacting with tubulin. Thermophoresis assays using scoulerine and tubulin in both free and polymerized form confirm these computational predictions. We conclude that scoulerine exhibits a unique property of a dual mode of action with both microtubule stabilization and tubulin polymerization inhibition, both of which have similar affinity values.

scholarly journals Computational Prediction and Experimental Validation of a Novel Binding Site for Platelet Integrin AlphaIIb-Beta3

2010 ◽  
Vol 98 (3) ◽  
pp. 40a
Author(s):  
Ana Negri ◽  
Davide Provasi ◽  
Jieqing Zhu ◽  
Jianghai Zhu ◽  
Barry S. Coller ◽  
...  
Keyword(s):  
Binding Site ◽  
Experimental Validation ◽  
Computational Prediction

Covalent-Fragment Screening of Brd4 Identifies a Ligandable Site Orthogonal to the Acetyl-Lysine Binding Sites

2019 ◽  
Author(s):  
Michael Olp ◽  
Daniel Sprague ◽  
Stefan Kathman ◽  
Ziyang Xu ◽  
Alexandar Statsyuk ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Binding Site ◽  
Binding Sites ◽  
Computational Prediction ◽  
Chemical Probes ◽  
Computational Docking ◽  
Fragment Screening ◽  
Covalent Inhibitors ◽  
Bet Protein ◽  
Proof Of Principle

<p>Brd4, a member of the bromodomain and extraterminal domain (BET) family, has emerged as a promising epigenetic target in cancer and inflammatory disorders. All reported BET family ligands bind within the bromodomain acetyl-lysine binding sites and competitively inhibit BET protein interaction with acetylated chromatin. Alternative chemical probes that act orthogonally to the highly-conserved acetyl-lysine binding sites may exhibit selectivity within the BET family and avoid recently reported toxicity in clinical trials of BET bromodomain inhibitors. Here, we report the first identification of a ligandable site on a bromodomain outside the acetyl-lysine binding site. Inspired by our computational prediction of hotspots adjacent to non-homologous cysteine residues within the <i>C</i>-terminal Brd4 bromodomain (Brd4-BD2), we performed a mid-throughput mass spectrometry screen to identify cysteine-reactive fragments that covalently and selectively modify Brd4. Subsequent mass spectrometry, NMR and computational docking analyses of electrophilic fragment hits revealed a novel ligandable site near Cys356 that is unique to Brd4 among all human bromodomains. This site is orthogonal to the Brd4-BD2 acetyl-lysine binding site as Cys356 modification did not impact binding of the pan-BET bromodomain inhibitor JQ1 in fluorescence polarization assays. Finally, we tethered covalent fragments to JQ1 and performed NanoBRET assays to provide proof of principle that this orthogonal site can be covalently targeted in intact human cells. Overall, we demonstrate the potential of targeting sites orthogonal to bromodomain acetyl-lysine binding sites to develop bivalent and covalent inhibitors that displace Brd4 from chromatin.</p>

Synthesis, Anti-proliferative Evaluation, and Molecular Docking Studies of 3-(alkylthio)-5,6-diaryl-1,2,4-triazines as Tubulin Polymerization Inhibitors

2019 ◽  
Vol 16 (11) ◽  
pp. 1194-1201 ◽  
Author(s):  
Farhad Saravani ◽  
Ebrahim Saeedian Moghadam ◽  
Hafezeh Salehabadi ◽  
Seyednasser Ostad ◽  
Morteza Pirali Hamedani ◽  
...  
Keyword(s):  
Molecular Modeling ◽  
Cytotoxic Activity ◽  
Binding Site ◽  
Cell Line ◽  
Cell Lines ◽  
Tubulin Polymerization ◽  
Adenocarcinoma Cell Line ◽  
Adenocarcinoma Cell ◽  
Colchicine Binding Site ◽  
Anti Cancer

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.

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

1991 ◽  
Vol 56 (11) ◽  
pp. 2306-2312 ◽  
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.

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

RSC Advances ◽  
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.

Monepantel: the most studied new anthelmintic drug of recent years

Parasitology ◽  
2014 ◽  
Vol 141 (13) ◽  
pp. 1686-1698 ◽  
Author(s):  
L. LECOVÁ ◽  
L. STUCHLÍKOVÁ ◽  
L. PRCHAL ◽  
L. SKÁLOVÁ
Keyword(s):  
Mode Of Action ◽  
Aquatic Organisms ◽  
Similar Efficacy ◽  
Gastrointestinal Nematodes ◽  
Soil Microflora ◽  
Parent Molecule ◽  
Important Species ◽  
Anthelmintic Drug ◽  
Reported Data ◽  
Molecular Mode

SUMMARYMonepantel (MOP), a new anthelmintic drug from a group of amino-acetonitrile derivatives, has been intensively studied during last years. Many authors examined this new drug from different perspectives, e.g. efficacy against different species and stages of parasites, mode of action, metabolism, pharmacokinetics, toxicity, resistance, ecotoxicity, etc. MOP is an anthelmintic for livestock (currently only sheep and goats), with molecular mode of action which is different to all other anthelmintics. MOP has a broad-spectrum of activity against gastrointestinal nematodes of sheep, including adults and L4 larvae of the most important species. The key feature of MOP is its full effectiveness against strains of nematodes resistant to benzimidazoles, levamisole, macrocyclic lactones and closantel. After oral administration, MOP is quickly absorbed into the bloodstream and quickly metabolized to MOP sulfone that has a similar efficacy as the parent molecule. Several other MOP metabolites formed in ovine hepatocytes were described. MOP and its metabolites are considered to be non-toxic to environment and its components, such as soil microflora, aquatic organisms, dung organisms, vegetation, etc. The aim of the presented review was not to collect all reported data but to bring an overview of various approaches in the study of MOP and to evaluate their principal results.

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