Change search
ReferencesLink to record
Permanent link

Direct link
Structural and Energetic Effects of A2A Adenosine Receptor Mutations on Agonist and Antagonist Binding
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational and Systems Biology. (Johan Åqvist)
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.
2014 (English)In: PLoS ONE, ISSN 1932-6203, Vol. 9, no 10, e108492- p.Article in journal (Refereed) Published
Abstract [en]

To predict structural and energetic effects of point mutations on ligand binding is of considerable interest in biochemistry and pharmacology. This is not only useful in connection with site-directed mutagenesis experiments, but could also allow interpretation and prediction of individual responses to drug treatment. For G-protein coupled receptors systematic mutagenesis has provided the major part of functional data as structural information until recently has been very limited. For the pharmacologically important A(2A) adenosine receptor, extensive site-directed mutagenesis data on agonist and antagonist binding is available and crystal structures of both types of complexes have been determined. Here, we employ a computational strategy, based on molecular dynamics free energy simulations, to rationalize and interpret available alanine-scanning experiments for both agonist and antagonist binding to this receptor. These computer simulations show excellent agreement with the experimental data and, most importantly, reveal the molecular details behind the observed effects which are often not immediately evident from the crystal structures. The work further provides a distinct validation of the computational strategy used to assess effects of point-mutations on ligand binding. It also highlights the importance of considering not only protein-ligand interactions but also those mediated by solvent water molecules, in ligand design projects.

Place, publisher, year, edition, pages
2014. Vol. 9, no 10, e108492- p.
National Category
Biological Sciences Chemical Sciences
URN: urn:nbn:se:uu:diva-230775DOI: 10.1371/journal.pone.0108492ISI: 000345743700022PubMedID: 25285959OAI: diva2:741757
Available from: 2014-08-29 Created: 2014-08-29 Last updated: 2015-01-23Bibliographically approved
In thesis
1. Advances in Ligand Binding Predictions using Molecular Dynamics Simulations
Open this publication in new window or tab >>Advances in Ligand Binding Predictions using Molecular Dynamics Simulations
2014 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Biochemical processes all involve associations and dissociations of chemical entities. Understanding these is of substantial importance for many modern pharmaceutical applications. In this thesis, longstanding problems with regard to ligand binding are treated with computational methods, applied to proteins of key pharmaceutical importance. Homology modeling, docking, molecular dynamics simulations and free-energy calculations are used here for quantitative characterization of ligand binding to proteins. By combining computational tools, valuable contributions have been made for pharmaceutically relevant areas: a neglected tropical disease, an ion channel anti-drug-target, and GPCR drug-targets.

We report three compounds inhibiting cruzain, the main cysteine protease of the protozoa causing Chagas’ disease. The compounds were found through an extensive virtual screening study and validated with experimental enzymatic assays. The compounds inhibit the enzyme in the μM-range and are therefore valuable in further lead optimization studies.

A high-resolution crystal structure of the BRICHOS domain is reported, together with molecular dynamics simulations and hydrogen-deuterium exchange mass spectrometry studies. This work revealed a plausible mechanism for how the chaperone activity of the domain may operate.

Rationalization of structure-activity relationships for a set of analogous blockers of the hERG potassium channel is given. A homology model of the ion channel was used for docking compounds and molecular dynamics simulations together with the linear interaction energy method employed for calculating the binding free-energies.

The three-dimensional coordinates of two GPCRs, 5HT1B and 5HT2B, were derived from homology modeling and evaluated in the GPCR Dock 2013 assessment. Our models were in good correlation with the experimental structures and all of them placed among the top quarter of all models assessed. 

Finally, a computational method, based on molecular dynamics free-energy calculations, for performing alanine scanning was validated with the A2A adenosine receptor bound to either agonist or antagonist. The calculated binding free-energies were found to be in good agreement with experimental data and the method was subsequently extended to non-alanine mutations. With extensive experimental mutation data, this scheme is a valuable tool for quantitative understanding of ligand binding and can ultimately be used for structure-based drug design.

Place, publisher, year, edition, pages
Uppsala: Uppsala universitet, 2014. 51 p.
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1651-6214 ; 1172
free-energy perturbation, molecular dynamics, ligand binding, free-energy perturbation, linear interaction energy, binding free-energy, homology modeling, virtual screening, alanine scanning, amino acid mutagenesis, hERG, GPCR, adenosine receptor, serotonin receptor, BRICHOS, cruzain
National Category
Theoretical Chemistry Biological Sciences
urn:nbn:se:uu:diva-230777 (URN)978-91-554-9020-1 (ISBN)
Public defence
2014-10-15, B41, BMC, Husargatan 3, Uppsala, 13:15 (English)
Available from: 2014-09-23 Created: 2014-08-29 Last updated: 2015-01-23

Open Access in DiVA

fulltext(3854 kB)74 downloads
File information
File name FULLTEXT02.pdfFile size 3854 kBChecksum SHA-512
Type fulltextMimetype application/pdf

Other links

Publisher's full textPubMed

Search in DiVA

By author/editor
Keränen, HenrikGutiérrez-de-Terán, HugoÅqvist, Johan
By organisation
Computational and Systems Biology
In the same journal
Biological SciencesChemical Sciences

Search outside of DiVA

GoogleGoogle Scholar
Total: 74 downloads
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: 296 hits
ReferencesLink to record
Permanent link

Direct link