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Berg, Lotta
Alternative names
Publications (10 of 11) Show all publications
Berg, L. (2017). Exploring non-covalent interactions between drug-like molecules and the protein acetylcholinesterase. (Doctoral dissertation). Umeå: Umeå universitet
Open this publication in new window or tab >>Exploring non-covalent interactions between drug-like molecules and the protein acetylcholinesterase
2017 (English)Doctoral thesis, comprehensive summary (Other academic)
Alternative title[sv]
En studie av icke-kovalenta interaktioner mellan läkemedelslika molekyler och proteinet acetylkolinesteras
Abstract [en]

The majority of drugs are small organic molecules, so-called ligands, that influence biochemical processes by interacting with proteins. The understanding of how and why they interact and form complexes is therefore a key component for elucidating the mechanism of action of drugs. The research presented in this thesis is based on studies of acetylcholinesterase (AChE). AChE is an essential enzyme with the important function of terminating neurotransmission at cholinergic synapses. AChE is also the target of a range of biologically active molecules including drugs, pesticides, and poisons. Due to the molecular and the functional characteristics of the enzyme, it offers both challenges and possibilities for investigating protein-ligand interactions. In the thesis, complexes between AChE and drug-like ligands have been studied in detail by a combination of experimental techniques and theoretical methods. The studies provided insight into the non-covalent interactions formed between AChE and ligands, where non-classical CH∙∙∙Y hydrogen bonds (Y = O or arene) were found to be common and important. The non-classical hydrogen bonds were characterized by density functional theory calculations that revealed features that may provide unexplored possibilities in for example structure-based design. Moreover, the study of two enantiomeric inhibitors of AChE provided important insight into the structural basis of enthalpy-entropy compensation. As part of the research, available computational methods have been evaluated and new approaches have been developed. This resulted in a methodology that allowed detailed analysis of the AChE-ligand complexes. Moreover, the methodology also proved to be a useful tool in the refinement of X-ray crystallographic data. This was demonstrated by the determination of a prereaction conformation of the complex between the nerve-agent antidote HI-6 and AChE inhibited by the nerve agent sarin. The structure of the ternary complex constitutes an important contribution of relevance for the design of new and improved drugs for treatment of nerve-agent poisoning. The research presented in the thesis has contributed to the knowledge of AChE and also has implications for drug discovery and the understanding of biochemical processes in general.

Place, publisher, year, edition, pages
Umeå: Umeå universitet, 2017. p. 76
Keywords
acetylcholinesterase, drug discovery, density functional theory, hydrogen bond, nerve-agent antidote, non-covalent interaction, protein-ligand complex, structure-based design, thermodynamics, X-ray crystallography
National Category
Chemical Sciences
Research subject
läkemedelskemi
Identifiers
urn:nbn:se:umu:diva-129900 (URN)978-91-7601-644-2 (ISBN)
Public defence
2017-02-03, Stora hörsalen (KB.E3.03), KBC-huset, Umeå universitet, Umeå, 10:00 (English)
Opponent
Supervisors
Available from: 2017-01-13 Created: 2017-01-10 Last updated: 2018-06-09Bibliographically approved
Allgardsson, A., Berg, L., Akfur, C., Hörnberg, A., Worek, F., Linusson, A. & Ekström, F. J. (2016). Structure of a prereaction complex between the nerve agent sarin, its biological target acetylcholinesterase, and the antidote HI-6. Proceedings of the National Academy of Sciences of the United States of America, 113(20), 5514-5519
Open this publication in new window or tab >>Structure of a prereaction complex between the nerve agent sarin, its biological target acetylcholinesterase, and the antidote HI-6
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2016 (English)In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 113, no 20, p. 5514-5519Article in journal (Refereed) Published
Abstract [en]

Organophosphorus nerve agents interfere with cholinergic signaling by covalently binding to the active site of the enzyme acetylcholinesterase (AChE). This inhibition causes an accumulation of the neurotransmitter acetylcholine, potentially leading to overstimulation of the nervous system and death. Current treatments include the use of antidotes that promote the release of functional AChE by an unknown reactivation mechanism. We have used diffusion trap cryocrystallography and density functional theory (DFT) calculations to determine and analyze prereaction conformers of the nerve agent antidote HI-6 in complex with Mus musculus AChE covalently inhibited by the nerve agent sarin. These analyses reveal previously unknown conformations of the system and suggest that the cleavage of the covalent enzyme-sarin bond is preceded by a conformational change in the sarin adduct itself. Together with data from the reactivation kinetics, this alternate conformation suggests a key interaction between Glu202 and the O-isopropyl moiety of sarin. Moreover, solvent kinetic isotope effect experiments using deuterium oxide reveal that the reactivation mechanism features an isotope-sensitive step. These findings provide insights into the reactivation mechanism and provide a starting point for the development of improved antidotes. The work also illustrates how DFT calculations can guide the interpretation, analysis, and validation of crystallographic data for challenging reactive systems with complex conformational dynamics.

Keywords
acetylcholinesterase, density functional theory, crystallography, nerve agent, reactivation
National Category
Chemical Sciences
Identifiers
urn:nbn:se:umu:diva-121442 (URN)10.1073/pnas.1523362113 (DOI)000375977600028 ()27140636 (PubMedID)
Available from: 2016-06-23 Created: 2016-06-02 Last updated: 2018-06-07Bibliographically approved
Berg, L., Mishra, B. K., Andersson, C. D., Ekström, F. & Linusson, A. (2016). The Nature of Activated Non-classical Hydrogen Bonds: A Case Study on Acetylcholinesterase-Ligand Complexes. Chemistry - A European Journal, 22(8), 2672-2681
Open this publication in new window or tab >>The Nature of Activated Non-classical Hydrogen Bonds: A Case Study on Acetylcholinesterase-Ligand Complexes
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2016 (English)In: Chemistry - A European Journal, ISSN 0947-6539, E-ISSN 1521-3765, Vol. 22, no 8, p. 2672-2681Article in journal (Refereed) Published
Abstract [en]

Molecular recognition events in biological systems are driven by non-covalent interactions between interacting species. Here, we have studied hydrogen bonds of the CHY type involving electron-deficient CH donors using dispersion-corrected density functional theory (DFT) calculations applied to acetylcholinesterase-ligand complexes. The strengths of CHY interactions activated by a proximal cation were considerably strong; comparable to or greater than those of classical hydrogen bonds. Significant differences in the energetic components compared to classical hydrogen bonds and non-activated CHY interactions were observed. Comparison between DFT and molecular mechanics calculations showed that common force fields could not reproduce the interaction energy values of the studied hydrogen bonds. The presented results highlight the importance of considering CHY interactions when analysing protein-ligand complexes, call for a review of current force fields, and opens up possibilities for the development of improved design tools for drug discovery.

Place, publisher, year, edition, pages
Wiley-VCH Verlagsgesellschaft, 2016
Keywords
acetylcholinesterase, density functional calculations, drug design, hydrogen bonds, quantum chemistry
National Category
Chemical Sciences
Identifiers
urn:nbn:se:umu:diva-118248 (URN)10.1002/chem.201503973 (DOI)000370193000017 ()26751405 (PubMedID)
Available from: 2016-03-16 Created: 2016-03-14 Last updated: 2018-06-07Bibliographically approved
Andersson, C. D., Hillgren, J. M., Lindgren, C., Qian, W., Akfur, C., Berg, L., . . . Linusson, A. (2015). Benefits of statistical molecular design, covariance analysis, and reference models in QSAR: a case study on acetylcholinesterase. Journal of Computer-Aided Molecular Design, 29(3), 199-215
Open this publication in new window or tab >>Benefits of statistical molecular design, covariance analysis, and reference models in QSAR: a case study on acetylcholinesterase
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2015 (English)In: Journal of Computer-Aided Molecular Design, ISSN 0920-654X, E-ISSN 1573-4951, Vol. 29, no 3, p. 199-215Article in journal (Refereed) Published
Abstract [en]

Scientific disciplines such as medicinal- and environmental chemistry, pharmacology, and toxicology deal with the questions related to the effects small organic compounds exhort on biological targets and the compounds' physicochemical properties responsible for these effects. A common strategy in this endeavor is to establish structure-activity relationships (SARs). The aim of this work was to illustrate benefits of performing a statistical molecular design (SMD) and proper statistical analysis of the molecules' properties before SAR and quantitative structure-activity relationship (QSAR) analysis. Our SMD followed by synthesis yielded a set of inhibitors of the enzyme acetylcholinesterase (AChE) that had very few inherent dependencies between the substructures in the molecules. If such dependencies exist, they cause severe errors in SAR interpretation and predictions by QSAR-models, and leave a set of molecules less suitable for future decision-making. In our study, SAR- and QSAR models could show which molecular sub-structures and physicochemical features that were advantageous for the AChE inhibition. Finally, the QSAR model was used for the prediction of the inhibition of AChE by an external prediction set of molecules. The accuracy of these predictions was asserted by statistical significance tests and by comparisons to simple but relevant reference models.

Keywords
Acetylcholinesterase, AChE, Quantitative structure-activity relationship, QSAR, Statistical molecular sign, SMD, Covariance matrix, Descriptors, Correlation
National Category
Medicinal Chemistry
Identifiers
urn:nbn:se:umu:diva-101389 (URN)10.1007/s10822-014-9808-1 (DOI)000349888300001 ()25351962 (PubMedID)
Available from: 2015-07-07 Created: 2015-03-30 Last updated: 2018-06-07Bibliographically approved
Lindgren, C., Andersson, I. E., Berg, L., Dobritzsch, D., Ge, C., Haag, S., . . . Linusson, A. (2015). Hydroxyethylene isosteres introduced in type II collagen fragments substantially alter the structure and dynamics of class II MHC A(q)/glycopeptide complexes. Organic and biomolecular chemistry, 13(22), 6203-6216
Open this publication in new window or tab >>Hydroxyethylene isosteres introduced in type II collagen fragments substantially alter the structure and dynamics of class II MHC A(q)/glycopeptide complexes
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2015 (English)In: Organic and biomolecular chemistry, ISSN 1477-0520, E-ISSN 1477-0539, Vol. 13, no 22, p. 6203-6216Article in journal (Refereed) Published
Abstract [en]

Class II major histocompatibility complex (MHC) proteins are involved in initiation of immune responses to foreign antigens via presentation of peptides to receptors of CD4(+) T-cells. An analogous presentation of self-peptides may lead to autoimmune diseases, such as rheumatoid arthritis (RA). The glycopeptide fragment CII259-273, derived from type II collagen, is presented by A(q) MHCII molecules in the mouse and has a key role in development of collagen induced arthritis (CIA), a validated model for RA. We have introduced hydroxyethylene amide bond isosteres at the Ala(261)-Gly(262) position of CII259-273. Biological evaluation showed that A(q) binding and T cell recognition were dramatically reduced for the modified glycopeptides, although static models predicted similar binding modes as the native type II collagen fragment. Molecular dynamics (MD) simulations demonstrated that introduction of the hydroxyethylene isosteres disturbed the entire hydrogen bond network between the glycopeptides and A(q). As a consequence the hydroxyethylene isosteric glycopeptides were prone to dissociation from A(q) and unfolding of the beta(1)-helix. Thus, the isostere induced adjustment of the hydrogen bond network altered the structure and dynamics of A(q)/glycopeptide complexes leading to the loss of A(q) affinity and subsequent T cell response.

National Category
Organic Chemistry
Identifiers
urn:nbn:se:umu:diva-106519 (URN)10.1039/c5ob00395d (DOI)000355489600011 ()25960177 (PubMedID)
Available from: 2015-07-15 Created: 2015-07-14 Last updated: 2018-06-07Bibliographically approved
Andersson, C. D., Forsgren, N., Akfur, C., Allgardsson, A., Berg, L., Engdahl, C., . . . Linusson, A. (2013). Divergent Structure-Activity Relationships of Structurally Similar Acetylcholinesterase Inhibitors. Journal of Medicinal Chemistry, 56(19), 7615-7624
Open this publication in new window or tab >>Divergent Structure-Activity Relationships of Structurally Similar Acetylcholinesterase Inhibitors
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2013 (English)In: Journal of Medicinal Chemistry, ISSN 0022-2623, E-ISSN 1520-4804, Vol. 56, no 19, p. 7615-7624Article in journal (Refereed) Published
Abstract [en]

The molecular interactions between the enzyme acetylcholinesterase (AChE) and two compound classes consisting of N-[2-(diethylamino)ethyl]benzenesulfonamides and N-[2-(diethylamino)ethyl]benzenemethanesulfonamides have been investigated using organic synthesis, enzymatic assays, X-ray crystallography, and thermodynamic profiling. The inhibitors' aromatic properties were varied to establish structure activity relationships (SAR) between the inhibitors and the peripheral anionic site (PAS) of AChE. The two structurally similar compound classes proved to have distinctly divergent SARs in terms of their inhibition capacity of AChE. Eight X-ray structures revealed that the two sets have different conformations in PAS. Furthermore, thermodynamic profiles of the binding between compounds and AChE revealed class-dependent differences of the entropy/enthalpy contributions to the free energy of binding. Further development of the entropy-favored compound class resulted in the synthesis of the most potent inhibitor and an extension beyond the established SARs. The divergent SARs will be utilized to develop reversible inhibitors of AChE into reactivators of nerve agent-inhibited AChE.

Place, publisher, year, edition, pages
American Chemical Society (ACS), 2013
National Category
Pharmaceutical Chemistry Chemical Sciences
Identifiers
urn:nbn:se:umu:diva-83903 (URN)10.1021/jm400990p (DOI)000326367100013 ()
Funder
Swedish Research Council
Available from: 2013-12-11 Created: 2013-12-10 Last updated: 2018-06-08Bibliographically approved
Berg, L., Niemiec, M. S., Qian, W., Andersson, C. D., Wittung-Stafshede, P., Ekström, F. & Linusson, A. (2012). Similar but Different: Thermodynamic and Structural Characterization of a Pair of Enantiomers Binding to Acetylcholinesterase. Angewandte Chemie International Edition, 51(51), 12716-12720
Open this publication in new window or tab >>Similar but Different: Thermodynamic and Structural Characterization of a Pair of Enantiomers Binding to Acetylcholinesterase
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2012 (English)In: Angewandte Chemie International Edition, ISSN 1433-7851, E-ISSN 1521-3773, Vol. 51, no 51, p. 12716-12720Article in journal (Refereed) Published
Abstract [en]

Take a closer look: Unexpectedly, a pair of enantiomeric ligands proved to have similar binding affinities for acetylcholinesterase. Further studies indicated that the enantiomers exhibit different thermodynamic profiles. Analyses of the noncovalent interactions in the protein-ligand complexes revealed that these differences are partly due to nonclassical hydrogen bonds between the ligands and aromatic side chains of the protein.

Keywords
aromatic interactions, density functional calculations, molecular recognition, nonclassical hydrogen bonds, stereoselectivity
National Category
Chemical Sciences
Identifiers
urn:nbn:se:umu:diva-61594 (URN)10.1002/anie.201205113 (DOI)23161758 (PubMedID)
Available from: 2012-11-20 Created: 2012-11-20 Last updated: 2018-06-08Bibliographically approved
Lindström, A., Edvinsson, L., Johansson, A., Andersson, C. D., Andersson, I. E., Raubacher, F. & Linusson, A. (2011). Postprocessing of docked protein-ligand complexes using implicit solvation models. Journal of chemical information and modeling, 51(2), 267-282
Open this publication in new window or tab >>Postprocessing of docked protein-ligand complexes using implicit solvation models
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2011 (English)In: Journal of chemical information and modeling, ISSN 1549-960X (online), 1549-9596 (print), Vol. 51, no 2, p. 267-282Article in journal (Refereed) Published
Abstract [en]

Molecular docking plays an important role in drug discovery as a tool for the structure-based design of small organic ligands for macromolecules. Possible applications of docking are identification of the bioactive conformation of a protein−ligand complex and the ranking of different ligands with respect to their strength of binding to a particular target. We have investigated the effect of implicit water on the postprocessing of binding poses generated by molecular docking using MM-PB/GB-SA (molecular mechanics Poisson−Boltzmann and generalized Born surface area) methodology. The investigation was divided into three parts: geometry optimization, pose selection, and estimation of the relative binding energies of docked protein−ligand complexes. Appropriate geometry optimization afforded more accurate binding poses for 20% of the complexes investigated. The time required for this step was greatly reduced by minimizing the energy of the binding site using GB solvation models rather than minimizing the entire complex using the PB model. By optimizing the geometries of docking poses using the GBHCT+SA model then calculating their free energies of binding using the PB implicit solvent model, binding poses similar to those observed in crystal structures were obtained. Rescoring of these poses according to their calculated binding energies resulted in improved correlations with experimental binding data. These correlations could be further improved by applying the postprocessing to several of the most highly ranked poses rather than focusing exclusively on the top-scored pose. The postprocessing protocol was successfully applied to the analysis of a set of Factor Xa inhibitors and a set of glycopeptide ligands for the class II major histocompatibility complex (MHC) Aq protein. These results indicate that the protocol for the postprocessing of docked protein−ligand complexes developed in this paper may be generally useful for structure-based design in drug discovery.

Keywords
Solvation, docking, MMPBSA, MMGBSA, Post processing, pose optimization, Faxtor Xa, MHC
National Category
Chemical Sciences Organic Chemistry Theoretical Chemistry
Research subject
Organic Chemistry; läkemedelskemi
Identifiers
urn:nbn:se:umu:diva-39985 (URN)10.1021/ci100354x (DOI)21309544 (PubMedID)
Available from: 2011-03-01 Created: 2011-02-14 Last updated: 2018-06-08Bibliographically approved
Berg, L., Andersson, C. D., Artursson, E., Hornberg, A., Tunemalm, A.-K., Linusson, A. & Ekstrom, F. (2011). Targeting Acetylcholinesterase: Identification of Chemical Leads by High Throughput Screening, Structure Determination and Molecular Modeling. PLoS ONE, 6(11), Article ID e26039.
Open this publication in new window or tab >>Targeting Acetylcholinesterase: Identification of Chemical Leads by High Throughput Screening, Structure Determination and Molecular Modeling
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2011 (English)In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 6, no 11, article id e26039Article in journal (Refereed) Published
Abstract [en]

Acetylcholinesterase (AChE) is an essential enzyme that terminates cholinergic transmission by rapid hydrolysis of the neurotransmitter acetylcholine. Compounds inhibiting this enzyme can be used (inter alia) to treat cholinergic deficiencies (e. g. in Alzheimer's disease), but may also act as dangerous toxins (e. g. nerve agents such as sarin). Treatment of nerve agent poisoning involves use of antidotes, small molecules capable of reactivating AChE. We have screened a collection of organic molecules to assess their ability to inhibit the enzymatic activity of AChE, aiming to find lead compounds for further optimization leading to drugs with increased efficacy and/or decreased side effects. 124 inhibitors were discovered, with considerable chemical diversity regarding size, polarity, flexibility and charge distribution. An extensive structure determination campaign resulted in a set of crystal structures of protein-ligand complexes. Overall, the ligands have substantial interactions with the peripheral anionic site of AChE, and the majority form additional interactions with the catalytic site (CAS). Reproduction of the bioactive conformation of six of the ligands using molecular docking simulations required modification of the default parameter settings of the docking software. The results show that docking-assisted structure-based design of AChE inhibitors is challenging and requires crystallographic support to obtain reliable results, at least with currently available software. The complex formed between C5685 and Mus musculus AChE (C5685.mAChE) is a representative structure for the general binding mode of the determined structures. The CAS binding part of C5685 could not be structurally determined due to a disordered electron density map and the developed docking protocol was used to predict the binding modes of this part of the molecule. We believe that chemical modifications of our discovered inhibitors, biochemical and biophysical characterization, crystallography and computational chemistry provide a route to novel AChE inhibitors and reactivators.

Place, publisher, year, edition, pages
San Francisco: Public Library of Science, 2011
National Category
Biological Sciences
Identifiers
urn:nbn:se:umu:diva-52194 (URN)10.1371/journal.pone.0026039 (DOI)000298168100002 ()
Available from: 2012-02-14 Created: 2012-02-13 Last updated: 2018-06-08Bibliographically approved
Andersson, I. E., Batsalova, T., Dzhambazov, B., Edvinsson, L., Holmdahl, R., Kihlberg, J. & Linusson, A. (2010). Oxazole-modified glycopeptides that target arthritis-associated class II MHC Aq and DR4 proteins. Organic and biomolecular chemistry, 8(13), 2931-2940
Open this publication in new window or tab >>Oxazole-modified glycopeptides that target arthritis-associated class II MHC Aq and DR4 proteins
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2010 (English)In: Organic and biomolecular chemistry, ISSN 1477-0520, E-ISSN 1477-0539, Vol. 8, no 13, p. 2931-2940Article in journal (Refereed) Published
Abstract [en]

The glycopeptide CII259-273, a fragment from type II collagen (CII), can induce tolerance in mice susceptible to collagen-induced arthritis (CIA), which is a validated disease model for rheumatoid arthritis (RA). Here, we describe the design and synthesis of a small series of modified CII259-273 glycopeptides with oxazole heterocycles replacing three potentially labile peptide bonds. These glycopeptidomimetics were evaluated for binding to murine CIA-associated A(q) and human RA-associated DR4 class II major histocompatibility complex (MHC) proteins. The oxazole modifications drastically reduced or completely abolished binding to A(q). Two of the glycopeptidomimetics were, however, well tolerated in binding to DR4 and they also induced strong responses by one or two DR4-restricted T-cell hybridomas. This work contributes to the development of an altered glycopeptide for inducing immunological tolerance in CIA, with the long-term goal of developing a therapeutic vaccine for treatment of RA.

Place, publisher, year, edition, pages
RSC Publishing, 2010
Identifiers
urn:nbn:se:umu:diva-35270 (URN)10.1039/c003640d (DOI)000278824700008 ()20485848 (PubMedID)
Available from: 2010-08-11 Created: 2010-08-11 Last updated: 2018-06-08Bibliographically approved
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