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Wiklander, Jesper G.
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Nicholls, I. A., Olsson, G. D., Karlsson, B. C. G., Suriyanarayanan, S. & Wiklander, J. G. (2018). Theoretical and Computational Strategies in Molecularly Imprinted Polymer Development. In: Wlodzimierz Kutner, Piyush Sindhu Sharma (Ed.), Molecularly Imprinted Polymers for Analytical Chemistry Applications: (pp. 197-226). London: Royal Society of Chemistry
Open this publication in new window or tab >>Theoretical and Computational Strategies in Molecularly Imprinted Polymer Development
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2018 (English)In: Molecularly Imprinted Polymers for Analytical Chemistry Applications / [ed] Wlodzimierz Kutner, Piyush Sindhu Sharma, London: Royal Society of Chemistry, 2018, p. 197-226Chapter in book (Refereed)
Abstract [en]

Theoretical and computational studies of molecular imprinting have helped provide valuable insights concerning the nature of the molecular-level events underlying the recognition characteristics of molecularly imprinted materials. Here, we first present an overview of a thermodynamic treatment of factors governing the behaviour of these functional materials, and then a summary of the development and current status of the use of computational strategies for studying aspects of molecular imprinting and the resulting material properties.

Place, publisher, year, edition, pages
London: Royal Society of Chemistry, 2018
Series
Polymer Chemistry Series
National Category
Theoretical Chemistry
Research subject
Chemistry, Organic Chemistry
Identifiers
urn:nbn:se:lnu:diva-81879 (URN)10.1039/9781788010474-00197 (DOI)2-s2.0-85047140306 (Scopus ID)978-1-78262-647-3 (ISBN)978-1-78801-047-4 (ISBN)978-1-78801-427-4 (ISBN)
Available from: 2019-04-12 Created: 2019-04-12 Last updated: 2019-08-29Bibliographically approved
Chavan, S., Abdelaziz, A., Wiklander, J. G. & Nicholls, I. A. (2016). A k-nearest neighbor classification of hERG K+ channel blockers. Journal of Computer-Aided Molecular Design, 30(3), 229-236
Open this publication in new window or tab >>A k-nearest neighbor classification of hERG K+ channel blockers
2016 (English)In: Journal of Computer-Aided Molecular Design, ISSN 0920-654X, E-ISSN 1573-4951, Vol. 30, no 3, p. 229-236Article in journal (Refereed) Published
Abstract [en]

A series of 172 molecular structures that block the hERG K+ channel were used to develop a classification model where, initially, eight types of PaDEL fingerprints were used for k-nearest neighbor model development. A consensus model constructed using Extended-CDK, PubChem and Substructure count fingerprint-based models was found to be a robust predictor of hERG activity. This consensus model demonstrated sensitivity and specificity values of 0.78 and 0.61 for the internal dataset compounds and 0.63 and 0.54 for the external (PubChem) dataset compounds, respectively. This model has identified the highest number of true positives (i.e. 140) from the PubChem dataset so far, as compared to other published models, and can potentially serve as a basis for the prediction of hERG active compounds. Validating this model against FDA-withdrawn substances indicated that it may even be useful for differentiating between mechanisms underlying QT prolongation.

Keywords
Classification model, hERG blockers, Ikr, KCNH2, k-nearest neighbor (k-NN), Toxicity
National Category
Bioinformatics (Computational Biology)
Research subject
Chemistry, Medical Chemistry
Identifiers
urn:nbn:se:lnu:diva-52222 (URN)10.1007/s10822-016-9898-z (DOI)000373117200004 ()26860111 (PubMedID)2-s2.0-84957695003 (Scopus ID)
Available from: 2016-04-25 Created: 2016-04-25 Last updated: 2018-11-02Bibliographically approved
Shoravi, S., Olsson, G. D., Karlsson, B. C. G., Bexborn, F., Abghoui, Y., Hussain, J., . . . Nicholls, I. A. (2016). In silico screening of molecular imprinting prepolymerization systems: oseltamivir selective polymers through full-system molecular dynamics-based studies. Organic and biomolecular chemistry, 14(18), 4210-4219
Open this publication in new window or tab >>In silico screening of molecular imprinting prepolymerization systems: oseltamivir selective polymers through full-system molecular dynamics-based studies
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2016 (English)In: Organic and biomolecular chemistry, ISSN 1477-0520, E-ISSN 1477-0539, Vol. 14, no 18, p. 4210-4219Article in journal (Refereed) Published
Abstract [en]

All-component molecular dynamics studies were used to probe a library of oseltamivir molecularly imprinted polymer prepolymerization mixtures. Polymers included one of five functional monomers (acrylamide, hydroxyethylmethacrylate, methacrylic acid, 2-(triflouromethyl)acrylic acid, 4-vinylpyridine) and one of three porogens (acetonitrile, chloroform, methanol) combined with the crosslinking agent ethylene glycol dimethacrylate and initiator 2,2'-azobis(2-methylpropionitrile). Polymers were characterized by nitrogen gas sorption measurements and SEM, and affinity studies performed using radioligand binding in various media. In agreement with the predictions made from the simulations, polymers prepared in acetonitrile using either methacrylic or trifluoromethacrylic acid demonstrated the highest affinities for oseltamivir. Further, the ensemble of interactions observed in the methanol system provided an explanation for the morphology of polymers prepared in this solvent. The materials developed here offer potential for use in solid-phase extraction or for catalysis. The results illustrate the strength of this in silico strategy as a potential prognostic tool in molecularly imprinted polymer design.

National Category
Organic Chemistry
Research subject
Chemistry, Organic Chemistry
Identifiers
urn:nbn:se:lnu:diva-53319 (URN)10.1039/c6ob00305b (DOI)000375610600007 ()2-s2.0-84967333692 (Scopus ID)
Available from: 2016-06-10 Created: 2016-06-10 Last updated: 2018-11-02Bibliographically approved
Golker, K., Karlsson, B. C. G., Wiklander, J. G., Rosengren, A. M. & Nicholls, I. A. (2015). Hydrogen bond diversity in the pre-polymerization stage contributes to morphology and MIP-template recognition–MAA versus MMA. European Polymer Journal, 66, 558-568
Open this publication in new window or tab >>Hydrogen bond diversity in the pre-polymerization stage contributes to morphology and MIP-template recognition–MAA versus MMA
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2015 (English)In: European Polymer Journal, ISSN 0014-3057, E-ISSN 1873-1945, Vol. 66, p. 558-568Article in journal (Refereed) Published
Abstract [en]

This report demonstrates that the diversity of hydrogen bond interactions present in molecularly imprinted polymer pre-polymerization mixtures, typically associated with binding-site heterogeneity, can also contribute to morphological characteristics that may influence polymer–template recognition. Comparisons have been made between a series of bupivacaine molecularly imprinted methacrylic acid (MAA)–ethylene glycol dimethacrylate (EGDMA) copolymers and a series of analogous methyl methacrylate (MMA)–EGDMA copolymers using comprehensive molecular dynamics studies of the respective pre-polymerization mixtures, template–polymer binding studies and detailed BET surface area and BJH porosity analyses. The role of the carboxylic acid functionality of MAA, and in particular the acidic proton, in generating morphological features conducive to analyte access (slit-like rather than ink bottle-like structures) and recognition is discussed.

Place, publisher, year, edition, pages
Pergamon Press, 2015
National Category
Materials Chemistry
Research subject
Chemistry, Organic Chemistry
Identifiers
urn:nbn:se:lnu:diva-42601 (URN)10.1016/j.eurpolymj.2015.03.018 (DOI)000353854000057 ()2-s2.0-84928389138 (Scopus ID)
Available from: 2015-04-15 Created: 2015-04-15 Last updated: 2018-11-02Bibliographically approved
Nicholls, I. A., Chavan, S., Golker, K., Karlsson, B. C. G., Olsson, G. D., Rosengren, A. M., . . . Wiklander, J. G. (2015). Theoretical and Computational Strategies for the Study of the Molecular Imprinting Process and Polymer Performance. In: Mattiasson, B. & Ye, L. (Ed.), Molecularly Imprinted Polymers in Biotechnology: (pp. 25-50). Berlin: Springer
Open this publication in new window or tab >>Theoretical and Computational Strategies for the Study of the Molecular Imprinting Process and Polymer Performance
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2015 (English)In: Molecularly Imprinted Polymers in Biotechnology / [ed] Mattiasson, B. & Ye, L., Berlin: Springer, 2015, p. 25-50Chapter in book (Refereed)
Abstract [en]

The development of in silico strategies for the study of the molecular imprinting process and the properties of molecularly imprinted materials has been driven by a growing awareness of the inherent complexity of these systems and even by an increased awareness of the potential of these materials for use in a range of application areas. Here we highlight the development of theoretical and computational strategies that are contributing to an improved understanding of the mechanisms underlying molecularly imprinted material synthesis and performance, and even their rational design.

Place, publisher, year, edition, pages
Berlin: Springer, 2015
Series
Advances in Biochemical Engineering-Biotechnology, ISSN 0724-6145 ; 150
National Category
Polymer Technologies
Research subject
Chemistry, Organic Chemistry
Identifiers
urn:nbn:se:lnu:diva-42600 (URN)10.1007/10_2015_318 (DOI)000365222300003 ()2-s2.0-84938411248 (Scopus ID)978-3-319-20729-2 (ISBN)978-3-319-20728-5 (ISBN)
Available from: 2015-04-15 Created: 2015-04-15 Last updated: 2018-11-02Bibliographically approved
Elmlund, L., Suriyanarayanan, S., Wiklander, J. G., Aastrup, T. & Nicholls, I. A. (2014). Biotin selective polymer nano-films. Journal of Nanobiotechnology, 12, Article ID 8.
Open this publication in new window or tab >>Biotin selective polymer nano-films
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2014 (English)In: Journal of Nanobiotechnology, ISSN 1477-3155, E-ISSN 1477-3155, Vol. 12, article id 8Article in journal (Refereed) Published
Abstract [en]

Background: The interaction between biotin and avidin is utilized in a wide range of assay and diagnostic systems. A robust material capable of binding biotin should offer scope in the development of reusable assay materials and biosensor recognition elements. Results: Biotin-selective thin (3-5 nm) films have been fabricated on hexadecanethiol self assembled monolayer (SAM) coated Au/quartz resonators. The films were prepared based upon a molecular imprinting strategy where N, N'-methylenebisacrylamide and 2-acrylamido-2-methylpropanesulfonic acid were copolymerized and grafted to the SAM-coated surface in the presence of biotin methyl ester using photoinitiation with physisorbed benzophenone. The biotinyl moiety selectivity of the resonators efficiently differentiated biotinylated peptidic or carbohydrate structures from their native counterparts. Conclusions: Molecularly imprinted ultra thin films can be used for the selective recognition of biotinylated structures in a quartz crystal microbalance sensing platform. These films are stable for periods of at least a month. This strategy should prove of interest for use in other sensing and assay systems.

Keywords
Molecularly imprinted polymer, Biotinylated compounds, Photoinitiated graft co-polymerization, Quartz crystal microbalance (QCM) sensors, Sandwich-casting method
National Category
Organic Chemistry
Research subject
Chemistry, Organic Chemistry
Identifiers
urn:nbn:se:lnu:diva-34479 (URN)10.1186/1477-3155-12-8 (DOI)000335075000001 ()2-s2.0-84899157003 (Scopus ID)
Available from: 2014-05-28 Created: 2014-05-28 Last updated: 2018-11-02Bibliographically approved
Nicholls, I. A., Andersson, H. S., Golker, K., Henschel, H., Karlsson, B. C. G., Olsson, G. D., . . . Wikman, S. (2013). Rational molecularly imprinted polymer design: theoretical and computational strategies. In: Ye, L (Ed.), Molecular Imprinting: Principles and Applications of Micro- and Nanostructured Polymers (pp. 71-104). London: Pan Stanford Publishing
Open this publication in new window or tab >>Rational molecularly imprinted polymer design: theoretical and computational strategies
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2013 (English)In: Molecular Imprinting: Principles and Applications of Micro- and Nanostructured Polymers / [ed] Ye, L, London: Pan Stanford Publishing, 2013, p. 71-104Chapter in book (Refereed)
Place, publisher, year, edition, pages
London: Pan Stanford Publishing, 2013
National Category
Organic Chemistry
Research subject
Chemistry, Organic Chemistry
Identifiers
urn:nbn:se:lnu:diva-8867 (URN)2-s2.0-84974679377 (Scopus ID)9789814310994 (ISBN)
Available from: 2010-10-08 Created: 2010-10-08 Last updated: 2018-11-02Bibliographically approved
Olsson, G. D., Karlsson, B. C. G., Shoravi, S., Wiklander, J. G. & Nicholls, I. A. (2012). Mechanisms Underlying Molecularly Imprinted Polymer Molecular Memory and The Role of Crosslinker: Resolving Debate on the Nature of Template Recognition in Phenylalanine Anilide Imprinted Polymers. Journal of Molecular Recognition, 25(2), 69-73
Open this publication in new window or tab >>Mechanisms Underlying Molecularly Imprinted Polymer Molecular Memory and The Role of Crosslinker: Resolving Debate on the Nature of Template Recognition in Phenylalanine Anilide Imprinted Polymers
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2012 (English)In: Journal of Molecular Recognition, ISSN 0952-3499, E-ISSN 1099-1352, Vol. 25, no 2, p. 69-73Article in journal (Refereed) Published
Abstract [en]

A series of molecular dynamics simulations of prepolymerization mixtures for phenylalanine anilide imprinted co-(ethylene glycol dimethacrylate-methacrylic acid) molecularly imprinted polymers have been employed to investigate the mechanistic basis for template selective recognition in these systems. This has provided new insights on the mechanisms underlying template recognition, in particular the significant role played by the crosslinking agent. Importantly, the study supports the occurrence of template self-association events that allows us to resolve debate between the two previously proposed models used to explain this system's underlying recognition mechanisms. Moreover, the complexity of the molecular level events underlying template complexation is highlighted by this study, a factor that should be considered in rational molecularly imprinted polymer design, especially with respect to recognition site heterogeneity.

National Category
Organic Chemistry Polymer Chemistry
Research subject
Chemistry, Organic Chemistry
Identifiers
urn:nbn:se:lnu:diva-16737 (URN)10.1002/jmr.2147 (DOI)2-s2.0-84856485453 (Scopus ID)
Available from: 2012-01-12 Created: 2012-01-12 Last updated: 2017-12-08Bibliographically approved
Nicholls, I. A., Andersson, H. S., Golker, K., Henschel, H., Karlsson, B. C. G., Olsson, G. D., . . . Wikman, S. (2011). Rational Design of Biomimetic Molecularly Imprinted Materials: Theoretical and Computational Strategies for Guiding Nanoscale Structured Polymer Development. Analytical and Bioanalytical Chemistry, 400, 1771-1786
Open this publication in new window or tab >>Rational Design of Biomimetic Molecularly Imprinted Materials: Theoretical and Computational Strategies for Guiding Nanoscale Structured Polymer Development
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2011 (English)In: Analytical and Bioanalytical Chemistry, ISSN 1618-2642, E-ISSN 1618-2650, Vol. 400, p. 1771-1786Article, review/survey (Refereed) Published
Abstract [en]

In principle, molecularly imprinted polymer science and technology provides a means for ready access to nano-structured polymeric materials of predetermined selectivity. The versatility of the technique has brought it to the attention of many working with the development of nanomaterials with biological or biomimetic properties for use as therapeutics or in medical devices. Nonetheless, the further evolution of the field necessitates the development of robust predictive tools capable of handling the complexity of molecular imprinting systems. The rapid growth in computer power and software over the past decade has opened new possibilities for simulating aspects of the complex molecular imprinting process. We present here a survey of the current status of the use of in silico-based approaches to aspects of molecular imprinting. Finally, we highlight areas where ongoing and future efforts should yield information critical to our understanding of the underlying mechanisms sufficient to permit the rational design of molecularly imprinted polymers.

National Category
Theoretical Chemistry Organic Chemistry Analytical Chemistry Polymer Chemistry
Research subject
Chemistry, Organic Chemistry
Identifiers
urn:nbn:se:lnu:diva-16276 (URN)10.1007/s00216-011-4935-1 (DOI)2-s2.0-84961983789 (Scopus ID)
Available from: 2011-12-21 Created: 2011-12-21 Last updated: 2018-05-18Bibliographically approved
Wiklander, J. G., Karlsson, B. C. G., Aastrup, T. & Nicholls, I. A. (2011). Towards a synthetic avidin mimic. Analytical and Bioanalytical Chemistry, 400(5), 1397-1404
Open this publication in new window or tab >>Towards a synthetic avidin mimic
2011 (English)In: Analytical and Bioanalytical Chemistry, ISSN 1618-2642, E-ISSN 1618-2650, Vol. 400, no 5, p. 1397-1404Article in journal (Refereed) Published
Abstract [en]

A series of streptavidin-mimicking molecularly imprinted polymers has been developed and evaluated for their biotin binding characteristics. A combination of molecular dynamics and NMR spectroscopy was used to examine potential polymer systems, in particular with the functional monomers methacrylic acid and 2-acrylamidopyridine. The synthesis of copolymers of ethylene dimethacrylate and one or both of these functional monomers was performed. A combination of radioligand binding studies and surface area analyses demonstrated the presence of selectivity in polymers prepared using methacrylic acid as the functional monomer. This was predicted by the molecular dynamics studies showing the power of this methodology as a prognostic tool for predicting the behavior of molecularly imprinted polymers.

National Category
Analytical Chemistry Organic Chemistry Polymer Chemistry Theoretical Chemistry
Research subject
Chemistry, Organic Chemistry
Identifiers
urn:nbn:se:lnu:diva-16275 (URN)10.1007/s00216-011-4907-5 (DOI)2-s2.0-79955560945 (Scopus ID)
Available from: 2011-12-21 Created: 2011-12-21 Last updated: 2017-12-08Bibliographically approved
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