uu.seUppsala University Publications
Change search
ReferencesLink to record
Permanent link

Direct link
New in silico insights into the inhibition of RNAP II by alpha-amanitin and the protective effect mediated by effective antidotes
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational and Systems Biology.
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational and Systems Biology.
Show others and affiliations
2014 (English)In: Journal of Molecular Graphics and Modelling, ISSN 1093-3263, E-ISSN 1873-4243, Vol. 51, 120-127 p.Article in journal (Refereed) Published
Abstract [en]

Poisonous alpha-amanitin-containing mushrooms are responsible for the major cases of fatalities after mushroom ingestion. alpha-Amanitin is known to inhibit the RNA polymerase II (RNAP II), although the underlying mechanisms are not fully understood. Benzylpenicillin, ceftazidime and silybin have been the most frequently used drugs in the management of alpha-amanitin poisoning, mostly based on empirical rationale. The present study provides an in silica insight into the inhibition of RNAP II by alpha-amanitin and also on the interaction of the antidotes on the active site of this enzyme. Docking and molecular dynamics (MD) simulations combined with molecular mechanics-generalized Born surface area method (MM-GBSA) were carried out to investigate the binding of alpha-amanitin and three antidotes benzylpenicillin, ceftazidime and silybin to RNAP II. Our results reveal that alpha-amanitin should affects RNAP II transcription by compromising trigger loop (TL) function. The observed direct interactions between alpha-amanitin and TL residues Leu1081, Asn1082, Thr1083, His1085 and G1y1088 alters the elongation process and thus contribute to the inhibition of RNAP II. We also present evidences that alpha-amanitin can interact directly with the bridge helix residues G1y819, Gly820 and Glu822, and indirectly with His816 and Phe815. This destabilizes the bridge helix, possibly causing RNAP II activity loss. We demonstrate that benzylpenicillin, ceftazidime and silybin are able to bind to the same site as alpha-amanitin, although not replicating the unique alpha-amanitin binding mode. They establish considerably less intermolecular interactions and the ones existing are essential confine to the bridge helix and adjacent residues. Therefore, the therapeutic effect of these antidotes does not seem to be directly related with binding to RNAP II. RNAP II alpha-amanitin binding site can be divided into specific zones with different properties providing a reliable platform for the structure-based drug design of novel antidotes for alpha-amatoxin poisoning. An ideal drug candidate should be a competitive RNAP II binder that interacts with Arg726, 11e756, Ala759, Gln760 and G1n767, but not with TL and bridge helix residues. 

Place, publisher, year, edition, pages
2014. Vol. 51, 120-127 p.
Keyword [en]
alpha-Amanitin, Benzylpenicillin, Ceftazidime, Silybin, RNA polymerase II, Trigger loop, Bridge helix
National Category
Biochemistry and Molecular Biology
URN: urn:nbn:se:uu:diva-231437DOI: 10.1016/j.jmgm.2014.05.002ISI: 000340321900014PubMedID: 24879323OAI: oai:DiVA.org:uu-231437DiVA: diva2:744776
Available from: 2014-09-08 Created: 2014-09-08 Last updated: 2014-09-08Bibliographically approved

Open Access in DiVA

No full text

Other links

Publisher's full textPubMed

Search in DiVA

By author/editor
Carvalho, Alexandra T. P.Dourado, Daniel F. A. R.Carvalho, Felix
By organisation
Computational and Systems Biology
In the same journal
Journal of Molecular Graphics and Modelling
Biochemistry and Molecular Biology

Search outside of DiVA

GoogleGoogle Scholar
The number of downloads is the sum of all downloads of full texts. It may include eg previous versions that are now no longer available

Altmetric score

Total: 194 hits
ReferencesLink to record
Permanent link

Direct link