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Advances in Ligand Binding Predictions using Molecular Dynamics Simulations
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational and Systems Biology. (Johan Åqvist)
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
Keyword [en]
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: urn:nbn:se:uu:diva-230777ISBN: 978-91-554-9020-1OAI: diva2:741767
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
List of papers
1. Computational Identification of Uncharacterized Cruzain Binding Sites
Open this publication in new window or tab >>Computational Identification of Uncharacterized Cruzain Binding Sites
2010 (English)In: PLoS Neglected Tropical Diseases, ISSN 1935-2727, E-ISSN 1935-2735, Vol. 4, no 5, e676- p.Article in journal (Refereed) Published
Abstract [en]

Chagas disease, caused by the unicellular parasite Trypanosoma cruzi, claims 50,000 lives annually and is the leading cause of infectious myocarditis in the world. As current antichagastic therapies like nifurtimox and benznidazole are highly toxic, ineffective at parasite eradication, and subject to increasing resistance, novel therapeutics are urgently needed. Cruzain, the major cysteine protease of Trypanosoma cruzi, is one attractive drug target. In the current work, molecular dynamics simulations and a sequence alignment of a non-redundant, unbiased set of peptidase C1 family members are used to identify uncharacterized cruzain binding sites. The two sites identified may serve as targets for future pharmacological intervention.

National Category
Biological Sciences Medical and Health Sciences
urn:nbn:se:uu:diva-136298 (URN)10.1371/journal.pntd.0000676 (DOI)000278601000007 ()
Available from: 2010-12-11 Created: 2010-12-11 Last updated: 2015-01-23Bibliographically approved
2. Novel Cruzain Inhibitors for the Treatment of Chagas' Disease
Open this publication in new window or tab >>Novel Cruzain Inhibitors for the Treatment of Chagas' Disease
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2012 (English)In: Chemical Biology and Drug Design, ISSN 1747-0277, Vol. 80, no 3, 398-405 p.Article in journal (Refereed) Published
Abstract [en]

The protozoan parasite Trypanosoma cruzi, the etiological agent of Chagas disease, affects millions of individuals and continues to be an important global health concern. The poor efficacy and unfavorable side effects of current treatments necessitate novel therapeutics. Cruzain, the major cysteine protease of T.similar to cruzi, is one potential novel target. Recent advances in a class of vinyl sulfone inhibitors are encouraging; however, as most potential therapeutics fail in clinical trials and both disease progression and resistance call for combination therapy with several drugs, the identification of additional classes of inhibitory molecules is essential. Using an exhaustive virtual-screening and experimental validation approach, we identify several additional small-molecule cruzain inhibitors. Further optimization of these chemical scaffolds could lead to the development of novel drugs useful in the treatment of Chagas disease.

Chagas' disease, computer-aided drug discovery, cruzain, cruzipain, cysteine protease inhibitor, Trypanosoma cruzi
National Category
Medical and Health Sciences
urn:nbn:se:uu:diva-179897 (URN)10.1111/j.1747-0285.2012.01416.x (DOI)000306664800007 ()
Available from: 2012-08-28 Created: 2012-08-27 Last updated: 2015-01-23Bibliographically approved
3. High-resolution structure of a BRICHOS domain and its implications for anti-amyloid chaperone activity on lung surfactant protein C
Open this publication in new window or tab >>High-resolution structure of a BRICHOS domain and its implications for anti-amyloid chaperone activity on lung surfactant protein C
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2012 (English)In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 109, no 7, 2325-2329 p.Article in journal (Refereed) Published
Abstract [en]

BRICHOS domains are encoded in >30 human genes, which are associated with cancer, neurodegeneration, and interstitial lung disease (ILD). The BRICHOS domain from lung surfactant protein C proprotein (proSP-C) is required for membrane insertion of SP-C and has anti-amyloid activity in vitro. Here, we report the 2.1 angstrom crystal structure of the human proSP-C BRICHOS domain, which, together with molecular dynamics simulations and hydrogen-deuterium exchange mass spectrometry, reveals how BRICHOS domains may mediate chaperone activity. Observation of amyloid deposits composed of mature SP-C in lung tissue samples from ILD patients with mutations in the BRICHOS domain or in its peptide-binding linker region supports the in vivo relevance of the proposed mechanism. The results indicate that ILD mutations interfering with proSP-C BRICHOS activity cause amyloid disease secondary to intramolecular chaperone malfunction.

interstitial lung disease, SFTPC mutations, beta-sheet aggregates, transmembrane segment, discordant helix
National Category
Medical and Health Sciences
urn:nbn:se:uu:diva-171673 (URN)10.1073/pnas.1114740109 (DOI)000300489200038 ()
Available from: 2012-03-27 Created: 2012-03-25 Last updated: 2015-01-23Bibliographically approved
4. Computer Simulations of Structure-Activity Relationships for hERG Channel Blockers
Open this publication in new window or tab >>Computer Simulations of Structure-Activity Relationships for hERG Channel Blockers
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2011 (English)In: Biochemistry, ISSN 0006-2960, E-ISSN 1520-4995, Vol. 50, no 27, 6146-6156 p.Article in journal (Refereed) Published
Abstract [en]

The hERG potassium channel is of major pharmaceutical importance, and its blockade by various compounds, potentially causing serious cardiac side effects, is a major problem in drug development. Despite the large amounts of existing biochemical data on blockade of hERG by drugs and druglike compounds, relatively little is known regarding the structural basis of binding of blockers to the channel. Here, we have used a recently developed homology model of hERG to conduct molecular docking experiments with a series of channel blockers, followed by molecular dynamics simulations of the complexes and evaluation of binding free energies with the linear interaction energy method. The calculations yield a remarkably good agreement with experimental binding affinities and allow for a rationalization of three-dimensional structure-activity relationships in terms of a number of key interactions. Two main interaction regions of the channel are thus identified with implications for further mutagenesis experiments and design of new compounds.

National Category
Medical and Health Sciences
urn:nbn:se:uu:diva-156474 (URN)10.1021/bi200173n (DOI)000292430600018 ()
Available from: 2011-07-27 Created: 2011-07-25 Last updated: 2015-01-23Bibliographically approved
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6. Structural and Energetic Effects of A2A Adenosine Receptor Mutations on Agonist and Antagonist Binding
Open this publication in new window or tab >>Structural and Energetic Effects of A2A Adenosine Receptor Mutations on Agonist and Antagonist Binding
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.

National Category
Biological Sciences Chemical Sciences
urn:nbn:se:uu:diva-230775 (URN)10.1371/journal.pone.0108492 (DOI)000345743700022 ()25285959 (PubMedID)
Available from: 2014-08-29 Created: 2014-08-29 Last updated: 2015-01-23Bibliographically approved

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