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  • 1.
    Adbo, Karina
    et al.
    Högskolan i Kalmar, Naturvetenskapliga institutionen.
    Andersson, Håkan S.
    Högskolan i Kalmar, Naturvetenskapliga institutionen.
    Ankarloo, Jonas
    Högskolan i Kalmar, Naturvetenskapliga institutionen.
    Karlsson, Jesper G.
    Högskolan i Kalmar, Naturvetenskapliga institutionen.
    Norell, M C
    Olofsson, Linus
    Högskolan i Kalmar, Naturvetenskapliga institutionen.
    Svenson, Johan
    Högskolan i Kalmar, Naturvetenskapliga institutionen.
    Örtegren, U
    Nicholls, Ian A.
    Högskolan i Kalmar, Naturvetenskapliga institutionen.
    Enantioselective synthetic receptors for Tröger’s base1999Inngår i: Bioorganic Chemistry, Vol. 27, nr 5, s. 363-371Artikkel i tidsskrift (Fagfellevurdert)
  • 2.
    Adbo, Karina
    et al.
    Högskolan i Kalmar, Naturvetenskapliga institutionen.
    Nicholls, Ian Alan
    Högskolan i Kalmar, Naturvetenskapliga institutionen.
    Enantioselective SPE on Tröger’s base molecularly imprinted polymers2001Konferansepaper (Fagfellevurdert)
  • 3.
    Adbo, Karina
    et al.
    Högskolan i Kalmar, Naturvetenskapliga institutionen.
    Nicholls, Ian Alan
    Högskolan i Kalmar, Naturvetenskapliga institutionen.
    Study of the kinetics of enantioselective solid-phase extraction on Tröger’s base molecularly imprinted polymers2001Inngår i: Analytica Chimica Acta, Vol. 435, s. 115-120Artikkel i tidsskrift (Fagfellevurdert)
  • 4.
    Adbo, Karina
    et al.
    Högskolan i Kalmar, Naturvetenskapliga institutionen.
    Rosengren-Holmberg, Jenny
    Högskolan i Kalmar, Naturvetenskapliga institutionen.
    Nicholls, Ian Alan
    Högskolan i Kalmar, Naturvetenskapliga institutionen.
    Kinetics of enantioselective solid-phase extraction of Tröger’s base molecularly imprinted polymers2000Konferansepaper (Fagfellevurdert)
  • 5. Alexander, C
    et al.
    Andersson, Håkan S.
    Högskolan i Kalmar, Naturvetenskapliga institutionen.
    Andersson, L I
    Ansell, R I
    Kirsch, Nicole
    Högskolan i Kalmar, Naturvetenskapliga institutionen.
    Nicholls, Ian A.
    Högskolan i Kalmar, Naturvetenskapliga institutionen.
    O'Mahony, John
    Whitcombe, M J
    Molecular imprinting science and technology: a survey of the literature for the years up to and including 20032006Inngår i: Journal of molecular recognition, Vol. 19, nr 2, s. 106-180Artikkel i tidsskrift (Fagfellevurdert)
  • 6.
    Andersson, Håkan S.
    et al.
    Högskolan i Kalmar, Naturvetenskapliga institutionen.
    Karlsson, Jesper G.
    Högskolan i Kalmar, Naturvetenskapliga institutionen.
    Piletsky, S A
    Koch-Schmidt, Ann-Christin
    Högskolan i Kalmar, Naturvetenskapliga institutionen.
    Mosbach, K
    Nicholls, Ian A.
    Högskolan i Kalmar, Naturvetenskapliga institutionen.
    Influence of monomer-template ratio on selectivity and load capacity of molecularly imprinted polymers: indications of template self-association1999Inngår i: Journal of Chromatography A, Vol. 848, nr 1-2, s. 39-49Artikkel i tidsskrift (Fagfellevurdert)
  • 7.
    Andersson, Håkan S.
    et al.
    Högskolan i Kalmar, Naturvetenskapliga institutionen.
    Karlsson, Jesper G.
    Högskolan i Kalmar, Naturvetenskapliga institutionen.
    Svenson, Johan
    Högskolan i Kalmar, Naturvetenskapliga institutionen.
    Nicholls, Ian A.
    Högskolan i Kalmar, Naturvetenskapliga institutionen.
    Can template-template self-association contribute to polymer-ligand recognition characteristics?2000Konferansepaper (Fagfellevurdert)
  • 8.
    Andersson, Håkan S.
    et al.
    Högskolan i Kalmar, Naturvetenskapliga institutionen.
    Nicholls, Ian A.
    Högskolan i Kalmar, Naturvetenskapliga institutionen.
    Molecular Imprinting. Recent innovations in synthetic polymer receptor and enzyme mimics1997Inngår i: Recent Research Developments in Pure and Applied Chemistry, Vol. 1, s. 133-157Artikkel i tidsskrift (Fagfellevurdert)
  • 9.
    Andersson, Håkan S.
    et al.
    Högskolan i Kalmar, Naturvetenskapliga institutionen.
    Nicholls, Ian A.
    Högskolan i Kalmar, Naturvetenskapliga institutionen.
    Spectroscopic evaluation of molecular imprinting polymerization systems1997Inngår i: Bioorganic Chemistry, Vol. 25, s. 203-211Artikkel i tidsskrift (Fagfellevurdert)
  • 10.
    Andersson, Håkan S.
    et al.
    Högskolan i Kalmar, Naturvetenskapliga institutionen.
    Nicholls, Ian A.
    Högskolan i Kalmar, Naturvetenskapliga institutionen.
    The development of molecular imprinting2000Annet (Annet vitenskapelig)
  • 11.
    Andersson, Håkan S.
    et al.
    Högskolan i Kalmar, Naturvetenskapliga institutionen.
    Piletsky, S A
    Mosbach, K
    Koch-Schmidt, Ann-Christin
    Högskolan i Kalmar, Naturvetenskapliga institutionen.
    Nicholls, Ian A.
    Högskolan i Kalmar, Naturvetenskapliga institutionen.
    Novel recognition elements for improved molecularly imprinted polymer stereoselectivity1997Konferansepaper (Fagfellevurdert)
  • 12.
    Andersson, Håkan S.
    et al.
    Högskolan i Kalmar, Naturvetenskapliga institutionen.
    Piletsky, S A
    Nicholls, Ian A.
    Högskolan i Kalmar, Naturvetenskapliga institutionen.
    The role of electrostatic interactions in the enantioselective recognition of phenylalanine in molecularly imprinted polymers incorporating beta-cyclodextrin2005Inngår i: Polymer Journal, Vol. 37, s. 793-796Artikkel i tidsskrift (Fagfellevurdert)
  • 13.
    Andersson, Håkan S.
    et al.
    Högskolan i Kalmar, Naturvetenskapliga institutionen. Cranfield University, UK.
    Piletsky, Sergey A
    Högskolan i Kalmar, Naturvetenskapliga institutionen.
    Mosbach, Klaus
    Lund University.
    Nicholls, Ian A.
    Högskolan i Kalmar, Naturvetenskapliga institutionen.
    Koch-Schmidt, Ann-Christin
    Högskolan i Kalmar, Naturvetenskapliga institutionen.
    Cooperative Binding in Molecularly Imprinted Polymers against (-)-Nicotine.1997Konferansepaper (Annet vitenskapelig)
  • 14. Andersson, L I
    et al.
    Nicholls, Ian Alan
    Högskolan i Kalmar, Naturvetenskapliga institutionen.
    Molecular imprinting technology in separation science2004Inngår i: Journal of Chromatography B, Vol. 804 (1)Artikkel i tidsskrift (Fagfellevurdert)
  • 15. Andersson, L I
    et al.
    Nicholls, Ian Alan
    Högskolan i Kalmar, Naturvetenskapliga institutionen.
    Mosbach, K
    Immunoassays using molecularly imprinted polymers1995Inngår i: Immunoanalysis of agrochemicals: emerging technologies / [ed] Judd O. Nelson, Alexander E. Karu and Rosie B. Wong, American Chemical Society (ACS), 1995, s. 89-97Konferansepaper (Annet vitenskapelig)
  • 16. Andersson, L I
    et al.
    Nicholls, Ian Alan
    Högskolan i Kalmar, Naturvetenskapliga institutionen.
    Mosbach, K
    Molecular imprinting: the current status and future development of polymer-based recognition systems1996Inngår i: Advances in Molecular and Cell Biology, Vol. 15, s. 651-670Artikkel i tidsskrift (Fagfellevurdert)
  • 17.
    Ankarloo, Jonas
    et al.
    Högskolan i Kalmar, Naturvetenskapliga institutionen.
    Nicholls, Ian Alan
    Högskolan i Kalmar, Naturvetenskapliga institutionen.
    Escherichia coli viability in water-miscible organic solvents2001Konferansepaper (Fagfellevurdert)
  • 18.
    Ankarloo, Jonas
    et al.
    Högskolan i Kalmar, Naturvetenskapliga institutionen.
    Olofsson, Linus
    Högskolan i Kalmar, Naturvetenskapliga institutionen.
    Nicholls, Ian Alan
    Högskolan i Kalmar, Naturvetenskapliga institutionen.
    Phage viability in chemically extreme environments1997Konferansepaper (Fagfellevurdert)
  • 19.
    Ankarloo, Jonas
    et al.
    Linnéuniversitetet, Fakultetsnämnden för naturvetenskap och teknik, Institutionen för naturvetenskap, NV.
    Wikman, Susanne
    Linnéuniversitetet, Fakultetsnämnden för naturvetenskap och teknik, Institutionen för naturvetenskap, NV.
    Nicholls, Ian A.
    Linnéuniversitetet, Fakultetsnämnden för naturvetenskap och teknik, Institutionen för naturvetenskap, NV.
    Escherichia coli mar and acrAB Mutants Display No Tolerance to Simple Alcohols2010Inngår i: International Journal of Molecular Sciences, ISSN 1422-0067, E-ISSN 1422-0067, Vol. 11, nr 4, s. 1403-1412Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The inducible Mar phenotype of Escherichia coli is associated with increased tolerance to multiple hydrophobic antibiotics as well as some highly hydrophobic organic solvents such as cyclohexane, mediated mainly through the AcrAB/TolC efflux system. The influence of water miscible alcohols ethanol and 1-propanol on a Mar constitutive mutant and a mar deletion mutant of E. coli K-12, as well as the corresponding strains carrying the additional acrAB deletion, was investigated. In contrast to hydrophobic solvents, all strains were killed in exponential phase by 1-propanol and ethanol at rates comparable to the parent strain. Thus, the Mar phenotype does not protect E. coli from killing by these more polar solvents. Surprisingly, AcrAB does not contribute to an increased alcohol tolerance. In addition, sodium salicylate, at concentrations known to induce the mar operon, was unable to increase 1-propanol or ethanol tolerance. Rather, the toxicity of both solvents was increased in the presence of sodium salicylate. Collectively, the results imply that the resilience of E. coli to water miscible alcohols, in contrast to more hydrophobic solvents, does not depend upon the AcrAB/TolC efflux system, and suggests a lower limit for substrate molecular size and functionality. Implications for the application of microbiological systems in environments containing high contents of water miscible organic solvents, e. g., phage display screening, are discussed.

  • 20. Berglund, J
    et al.
    Lindbladh, C
    Nicholls, Ian Alan
    Högskolan i Kalmar, Naturvetenskapliga institutionen.
    Mosbach, K
    Selection of phage display combinatorial library peptides with affinity for a yohimbine imprinted methacrylate polymer1998Inngår i: Analytical Communications, Vol. 35, s. 3-7Artikkel i tidsskrift (Fagfellevurdert)
  • 21. Berglund, J
    et al.
    Nicholls, Ian Alan
    Högskolan i Kalmar, Naturvetenskapliga institutionen.
    Lindbladh, C
    Mosbach, K
    Recognition in molecularly imprinted polymer alpha 2-adrenoceptor mimics1996Inngår i: Bioorganic and Medicinal Chemistry Letters, Vol. 6, s. 2237-2242Artikkel i tidsskrift (Fagfellevurdert)
  • 22. Bunk, R
    et al.
    Klinth, Jeanna
    Högskolan i Kalmar, Naturvetenskapliga institutionen.
    Rosengren-Holmberg, Jenny
    Högskolan i Kalmar, Naturvetenskapliga institutionen.
    Nicholls, Ian Alan
    Högskolan i Kalmar, Naturvetenskapliga institutionen.
    Tågerud, Sven
    Högskolan i Kalmar, Naturvetenskapliga institutionen.
    Omling, P
    Montelius, L
    Månsson, Alf
    Högskolan i Kalmar, Naturvetenskapliga institutionen.
    An ordered in vitro motility assay for the study of actomyosin interactions.2002Konferansepaper (Fagfellevurdert)
  • 23. Bunk, R
    et al.
    Klinth, Jeanna
    Högskolan i Kalmar, Naturvetenskapliga institutionen.
    Rosengren-Holmberg, Jenny
    Högskolan i Kalmar, Naturvetenskapliga institutionen.
    Nicholls, Ian Alan
    Högskolan i Kalmar, Naturvetenskapliga institutionen.
    Tågerud, Sven
    Högskolan i Kalmar, Naturvetenskapliga institutionen.
    Omling, P
    Månsson, Alf
    Högskolan i Kalmar, Naturvetenskapliga institutionen.
    Montelius, L
    Imprinted tracks for biochemically powered motor proteins2002Konferansepaper (Fagfellevurdert)
  • 24. Bunk, R
    et al.
    Rosengren-Holmberg, Jenny
    Högskolan i Kalmar, Naturvetenskapliga institutionen.
    Frölander, Kerstin
    Montelius, L
    Nicholls, Ian Alan
    Högskolan i Kalmar, Naturvetenskapliga institutionen.
    Omling, P
    Tågerud, Sven
    Högskolan i Kalmar, Naturvetenskapliga institutionen.
    Månsson, Alf
    Högskolan i Kalmar, Naturvetenskapliga institutionen.
    Actomyosin motility on nanostructured resist polymers and silanes2003Konferansepaper (Fagfellevurdert)
  • 25. Bunk, R
    et al.
    Rosengren-Holmberg, Jenny
    Högskolan i Kalmar, Naturvetenskapliga institutionen.
    Nicholls, Ian Alan
    Högskolan i Kalmar, Naturvetenskapliga institutionen.
    Tågerud, Sven
    Högskolan i Kalmar, Naturvetenskapliga institutionen.
    Omling, P
    Månsson, Alf
    Högskolan i Kalmar, Naturvetenskapliga institutionen.
    Montelius, L
    Imprinted tracks for biochemically powered motor proteins?2002Konferansepaper (Fagfellevurdert)
  • 26. Bunk, R
    et al.
    Sundberg, Mark
    Högskolan i Kalmar, Naturvetenskapliga institutionen.
    Rosengren-Holmberg, Jenny
    Högskolan i Kalmar, Naturvetenskapliga institutionen.
    Carlberg, P
    Nicholls, Ian Alan
    Högskolan i Kalmar, Naturvetenskapliga institutionen.
    Tågerud, Sven
    Högskolan i Kalmar, Naturvetenskapliga institutionen.
    Omling, P
    Månsson, Alf
    Högskolan i Kalmar, Naturvetenskapliga institutionen.
    Montelius, L
    A biomolecular nanoscale traffic system: Controlled motion of quantum dot labelled motor proteins2004Annet (Annet vitenskapelig)
  • 27. Bunk, Richard
    et al.
    Carlberg, P
    Månsson, Alf
    Högskolan i Kalmar, Naturvetenskapliga institutionen.
    Nicholls, Ian Alan
    Högskolan i Kalmar, Naturvetenskapliga institutionen.
    Omling, Pär
    Sundberg, Mark
    Högskolan i Kalmar, Naturvetenskapliga institutionen.
    Tågerud, Sven
    Högskolan i Kalmar, Naturvetenskapliga institutionen.
    Montelius, Lars
    Guiding molecular motors with nano-imprinted structures2005Inngår i: Japanese journal of applied physics. Part 1, Regular papers, short notes & review papers, Vol. 44 (5A), s. 3337-3340Artikkel i tidsskrift (Fagfellevurdert)
  • 28. Bunk, Richard
    et al.
    Klinth, Jeanna
    Högskolan i Kalmar, Naturvetenskapliga institutionen.
    Montelius, Lars
    Nicholls, Ian Alan
    Högskolan i Kalmar, Naturvetenskapliga institutionen.
    Omling, Pär
    Tågerud, Sven
    Högskolan i Kalmar, Naturvetenskapliga institutionen.
    Månsson, Alf
    Högskolan i Kalmar, Naturvetenskapliga institutionen.
    Actomyosin motility on nanostructured surfaces2003Inngår i: Biochemical and Biophysical Research Communications, Vol. 301, s. 783-788Artikkel i tidsskrift (Fagfellevurdert)
  • 29. Bunk, Richard
    et al.
    Klinth, Jeanna
    Högskolan i Kalmar, Naturvetenskapliga institutionen.
    Rosengren-Holmberg, Jenny
    Högskolan i Kalmar, Naturvetenskapliga institutionen.
    Nicholls, Ian Alan
    Högskolan i Kalmar, Naturvetenskapliga institutionen.
    Tågerud, Sven
    Högskolan i Kalmar, Naturvetenskapliga institutionen.
    Omling, Pär
    Månsson, Alf
    Högskolan i Kalmar, Naturvetenskapliga institutionen.
    Montelius, Lars
    Towards a 'nano-traffic' system powered by molecular motors2003Inngår i: Microelectronic Engineering, Vol. 67-8, s. 899-904Artikkel i tidsskrift (Fagfellevurdert)
  • 30. Bunk, Richard
    et al.
    Sundberg, Mark
    Högskolan i Kalmar, Naturvetenskapliga institutionen.
    Månsson, Alf
    Högskolan i Kalmar, Naturvetenskapliga institutionen.
    Nicholls, Ian Alan
    Högskolan i Kalmar, Naturvetenskapliga institutionen.
    Omling, Pär
    Tågerud, Sven
    Högskolan i Kalmar, Naturvetenskapliga institutionen.
    Montelius, Lars
    Guiding motor-propelled molecules with nanoscale precision through silanized bi-channel structures2005Inngår i: Nanotechnology, Vol. 16 (6), s. 710-717Artikkel i tidsskrift (Fagfellevurdert)
  • 31.
    Bustin, Stephen A.
    et al.
    Anglia Ruskin University, UK.
    Nicholls, Ian A.
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för kemi och biomedicin (KOB).
    Iba, Michael
    Rutgers University, USA.
    International Journal of Molecular Science Best Paper Award 20142014Inngår i: International Journal of Molecular Sciences, ISSN 1422-0067, E-ISSN 1422-0067, Vol. 15, nr 1, s. 1683-1685Artikkel i tidsskrift (Annet vitenskapelig)
  • 32.
    Chavan, Swapnil
    et al.
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för kemi och biomedicin (KOB).
    Abdelaziz, Ahmed
    eADMET GmbH, Germany.
    Wiklander, Jesper G.
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för kemi och biomedicin (KOB).
    Nicholls, Ian A.
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för kemi och biomedicin (KOB). Uppsala University.
    A k-nearest neighbor classification of hERG K+ channel blockers2016Inngår i: Journal of Computer-Aided Molecular Design, ISSN 0920-654X, E-ISSN 1573-4951, Vol. 30, nr 3, s. 229-236Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 33.
    Chavan, Swapnil
    et al.
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för kemi och biomedicin (KOB).
    Friedman, Ran
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för kemi och biomedicin (KOB).
    Nicholls, Ian A.
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för kemi och biomedicin (KOB).
    Acute Toxicity-Supported Chronic Toxicity Prediction: A k-Nearest Neighbor Coupled Read-Across Strategy2015Inngår i: International Journal of Molecular Sciences, ISSN 1422-0067, E-ISSN 1422-0067, Vol. 16, nr 5, s. 11659-11677Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    k-nearest neighbor (k-NN) classification model was constructed for 118 RDT NEDO (Repeated Dose Toxicity New Energy and industrial technology Development Organization; currently known as the Hazard Evaluation Support System (HESS)) database chemicals, employing two acute toxicity (LD50)-based classes as a response and using a series of eight PaDEL software-derived fingerprints as predictor variables. A model developed using Estate type fingerprints correctly predicted the LD50 classes for 70 of 94 training set chemicals and 19 of 24 test set chemicals. An individual category was formed for each of the chemicals by extracting its corresponding k-analogs that were identified by k-NN classification. These categories were used to perform the read-across study for prediction of the chronic toxicity, i.e., Lowest Observed Effect Levels (LOEL). We have successfully predicted the LOELs of 54 of 70 training set chemicals (77%) and 14 of 19 test set chemicals (74%) to within an order of magnitude from their experimental LOEL values. Given the success thus far, we conclude that if the k-NN model predicts LD50classes correctly for a certain chemical, then the k-analogs of such a chemical can be successfully used for data gap filling for the LOEL. This model should support the in silico prediction of repeated dose toxicity.

  • 34.
    Chavan, Swapnil
    et al.
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för kemi och biomedicin (KOB).
    Nicholls, Ian A.
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för kemi och biomedicin (KOB). Uppsala University.
    Karlsson, Björn C. G.
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för kemi och biomedicin (KOB).
    Rosengren, Annika M.
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för kemi och biomedicin (KOB).
    Ballabio, Davide
    University of Milano-Bicocca, Italy.
    Consonni, Viviana
    University of Milano-Bicocca, Italy.
    Todeschini, Roberto
    University of Milano-Bicocca, Italy.
    Towards Global QSAR Model Building for Acute Toxicity: Munro Database Case Study2014Inngår i: International Journal of Molecular Sciences, ISSN 1422-0067, E-ISSN 1422-0067, Vol. 15, nr 10, s. 18162-18174Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    A series of 436 Munro database chemicals were studied with respect to their corresponding experimental LD50 values to investigate the possibility of establishing a global QSAR model for acute toxicity. Dragon molecular descriptors were used for the QSAR model development and genetic algorithms were used to select descriptors better correlated with toxicity data. Toxic values were discretized in a qualitative class on the basis of the Globally Harmonized Scheme: the 436 chemicals were divided into 3 classes based on their experimental LD50 values: highly toxic, intermediate toxic and low to non-toxic. The k-nearest neighbor (k-NN) classification method was calibrated on 25 molecular descriptors and gave a non-error rate (NER) equal to 0.66 and 0.57 for internal and external prediction sets, respectively. Even if the classification performances are not optimal, the subsequent analysis of the selected descriptors and their relationship with toxicity levels constitute a step towards the development of a global QSAR model for acute toxicity.

  • 35.
    Cleland, Dougal
    et al.
    The University of Newcastle, Australia.
    Olsson, Gustaf D.
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för kemi och biomedicin (KOB).
    Karlsson, Björn C. G.
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för kemi och biomedicin (KOB).
    Nicholls, Ian A.
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för kemi och biomedicin (KOB). Uppsala University.
    McCluskey, Adam
    The University of Newcastle, Australia.
    Molecular dynamics approaches to the design and synthesis of PCB targeting molecularly imprinted polymers: interference to monomer-template interactions in imprinting of 1,2,3-trichlorobenzene2014Inngår i: Organic and biomolecular chemistry, ISSN 1477-0520, E-ISSN 1477-0539, Vol. 12, nr 5, s. 844-853Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The interactions between each component of the pre-polymerisation mixtures used in the synthesis of molecularly imprinted polymers (MIP) specific for 1,2,3,4,5-pentachlorobenzene (1) and 1,2,3-trichlorobenzene (2) were examined in four molecular dynamics simulations. These simulations revealed that the relative frequency of functional monomer template (FM T) interactions was consistent with results obtained by the synthesis and evaluation of the actual MIPs. The higher frequency of 1 interaction with tri-methylstyrene (TMS; 54.7%) than 1 interaction with pentafluorostyrene (PFS; 44.7%) correlated with a higher imprinting factor (IF) of 2.1 vs. 1.7 for each functional monomer respectively. The higher frequency of PFS interactions with 2 (29.6%) than TMS interactions with 2 (1.9%) also correlated well with the observed differences in IF (3.7) of 2 MIPs imprinted using PFS as the FM than the IF (2,8) of 2 MIPs imprinted using TMS as the FM. The TMS-1 interaction dominated the molecular simulation due to high interaction energies, but the weaker TMS-2 resulted in low interaction maintenance, and thus lower IF values. Examination of the other pre-polymerisation mixture components revealed that the low levels of TMS-2 interaction was, in part, due to interference caused by the cross linker (CL) ethyleneglycol dimethylacrylate (EGDMA) interactions with TMS. The main reason was, however, attributed to MeOH interactions with TMS in both a hydrogen bond and perpendicular configuration. This positioned a MeOH directly above the it-orbital of all TMS for an average of 63.8% of MD2 creating significant interference to pi-pi stacking interactions between 2 and TMS. These findings are consistent with the deviation from the 'normal' molecularly imprinted polymer synthesis ratio of 1 : 4 : 20 (T : FM : CL) of 20 : 1 : 29 and 15 : 6 : 29 observed with 2 and TMS and PFS respectively. Our molecular dynamics simulations correctly predicted the high level of interference from other MIP synthesis components. The effect on PFS-1 interaction by MeOH was significantly lower and thus this system was not adversely affected.

  • 36.
    Elmlund, Louise
    et al.
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för kemi och biomedicin (KOB).
    Käck, Camilla
    Attana AB.
    Aastrup, Teodor
    Attana AB.
    Nicholls, Ian A.
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för kemi och biomedicin (KOB). Uppsala University.
    Study of the Interaction of Trastuzumab and SKOV3 Epithelial Cancer Cells Using a Quartz Crystal Microbalance Sensor2015Inngår i: Sensors, ISSN 1424-8220, E-ISSN 1424-8220, Vol. 15, nr 3, s. 5884-5894Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Analytical methods founded upon whole cell-based assays are of importance in early stage drug development and in fundamental studies of biomolecular recognition. Here we have studied the binding of the monoclonal antibody trastuzumab to human epidermal growth factor receptor 2 (HER2) on human ovary adenocarcinoma epithelial cancer cells (SKOV3) using quartz crystal microbalance (QCM) technology. An optimized procedure for immobilizing the cells on the chip surface was established with respect to fixation procedure and seeding density. Trastuzumab binding to the cell decorated sensor surface was studied, revealing a mean dissociation constant, K-D, value of 7 +/- 1 nM (standard error of the mean). This study provides a new perspective on the affinity of the antibody-receptor complex presented a more natural context compared to purified receptors. These results demonstrate the potential for using whole cell-based QCM assay in drug development, the screening of HER2 selective antibody-based drug candidates, and for the study of biomolecular recognition. This real time, label free approach for studying interactions with target receptors present in their natural environment afforded sensitive and detailed kinetic information about the binding of the analyte to the target.

  • 37.
    Elmlund, Louise
    et al.
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för kemi och biomedicin (KOB).
    Suriyanarayanan, Subramanian
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för kemi och biomedicin (KOB).
    Wiklander, Jesper G.
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för kemi och biomedicin (KOB).
    Aastrup, Teodor
    Attana AB, Stockholm.
    Nicholls, Ian A.
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för kemi och biomedicin (KOB). Uppsala University.
    Biotin selective polymer nano-films2014Inngår i: Journal of Nanobiotechnology, ISSN 1477-3155, E-ISSN 1477-3155, Vol. 12, artikkel-id 8Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 38.
    Elmlund, Louise
    et al.
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för kemi och biomedicin (KOB).
    Suriyanarayanan, Subramanian
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för kemi och biomedicin (KOB).
    Wiklander, Jesper
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för kemi och biomedicin (KOB).
    Nicholls, Ian A.
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för kemi och biomedicin (KOB). Uppsala University.
    Simple Strategy for Steering Polymer Film Formation on QCM Sensor SurfacesManuskript (preprint) (Annet vitenskapelig)
  • 39.
    Elmlund, Louise
    et al.
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för kemi och biomedicin (KOB).
    Söderberg, Pernilla
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM).
    Suriyanarayanan, Subramanian
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för kemi och biomedicin (KOB).
    Nicholls, Ian A.
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för kemi och biomedicin (KOB). Uppsala University.
    A Phage Display Screening Derived Peptide with Affinity for the Adeninyl Moiety2014Inngår i: Biosensors, ISSN 2079-6374, Vol. 4, nr 2, s. 137-149Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Phage display screening of a surface-immobilized adenine derivative led to the identification of a heptameric peptide with selectivity for adenine as demonstrated through quartz crystal microbalance (QCM) studies. The peptide demonstrated a concentration dependent affinity for an adeninyl moiety decorated surface (KD of 968 ± 53.3 μM), which highlights the power of piezoelectric sensing in the study of weak interactions. 

  • 40.
    Engberg, Anna E.
    et al.
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för kemi och biomedicin (KOB). Region Skåne.
    Nilsson, Per H.
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för kemi och biomedicin (KOB). Oslo Univ Hosp, Rikshosp, Norway;Univ Oslo, Norway.
    Huang, Shan
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för kemi och biomedicin (KOB).
    Fromell, Karin
    Uppsala University.
    Hamad, Osama A.
    Uppsala University.
    Mollnes, Tom Eirik
    Univ Oslo, Norway;Univ Tromsö, Norway.
    Rosengren-Holmberg, Jenny P.
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för kemi och biomedicin (KOB). Swedish Natl Lab Forens Sci, Linköping.
    Sandholm, Kerstin
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för kemi och biomedicin (KOB).
    Teramura, Yuji
    Uppsala University;Univ Tokyo, Japan.
    Nicholls, Ian A.
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för kemi och biomedicin (KOB). Uppsala University.
    Nilsson, Bo
    Uppsala University.
    Nilsson Ekdahl, Kristina
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för kemi och biomedicin (KOB). Uppsala University.
    Prediction of inflammatory responses induced by biomaterials in contact with human blood using protein fingerprint from plasma2015Inngår i: Biomaterials, ISSN 0142-9612, E-ISSN 1878-5905, Vol. 36, s. 55-65Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Inappropriate complement activation is often responsible for incompatibility reactions that occur when biomaterials are used. Complement activation is therefore a criterion included in legislation regarding biomaterials testing. However, no consensus is yet available regarding appropriate complement-activation-related test parameters. We examined protein adsorption in plasma and complement activation/cytokine release in whole blood incubated with well-characterized polymers. Strong correlations were found between the ratio of C4 to its inhibitor C4BP and generation of 10 (mainly pro-inflammatory) cytokines, including IL-17, IFN-gamma, and IL-6. The levels of complement activation products correlated weakly (C3a) or not at all (C5a, sC5b-9), confirming their poor predictive values. We have demonstrated a direct correlation between downstream biological effects and the proteins initially adhering to an artificial surface after contact with blood. Consequently, we propose the C4/C4BP ratio as a robust, predictor of biocompatibility with superior specificity and sensitivity over the current gold standard. (C) 2014 Elsevier Ltd. All rights reserved.

  • 41.
    Engberg, Anna E.
    et al.
    Linnéuniversitetet, Fakultetsnämnden för naturvetenskap och teknik, Institutionen för naturvetenskap, NV.
    Nilsson, Per H.
    Linnéuniversitetet, Fakultetsnämnden för naturvetenskap och teknik, Institutionen för naturvetenskap, NV.
    Mollnes, Tom Eirik
    Rosengren-Holmberg, Jenny P.
    Linnéuniversitetet, Fakultetsnämnden för naturvetenskap och teknik, Institutionen för naturvetenskap, NV.
    Nicholls, Ian A.
    Linnéuniversitetet, Fakultetsnämnden för naturvetenskap och teknik, Institutionen för naturvetenskap, NV.
    Nilsson, Bo
    Nilsson Ekdahl, Kristina
    Linnéuniversitetet, Fakultetsnämnden för naturvetenskap och teknik, Institutionen för naturvetenskap, NV.
    The ratio between C4 and C4BP adsorbed from plasma predicts cytokine generation induced by artificial polymers in contact with whole blood2012Inngår i: Immunobiology, ISSN 0171-2985, E-ISSN 1878-3279, Vol. 217, nr 11, s. 1211-1211Artikkel i tidsskrift (Annet vitenskapelig)
  • 42.
    Engberg, Anna E.
    et al.
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för kemi och biomedicin (KOB).
    Nilsson, Per H.
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för kemi och biomedicin (KOB). Univ Oslo, Rikshosp, Univ Hosp, Norway.
    Sandholm, Kerstin
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för kemi och biomedicin (KOB).
    Huang, Shan
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för kemi och biomedicin (KOB).
    Mollnes, T. E.
    Nicholls, Ian A.
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för kemi och biomedicin (KOB). Uppsala University.
    Nilsson, Bo
    Uppsala university.
    Nilsson Ekdahl, Kristina
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för kemi och biomedicin (KOB). Uppsala university.
    The ratio between C4 and C4BP adsorbed to artificial materials is a new predictor for biocompatibility2013Inngår i: Molecular Immunology, ISSN 0161-5890, E-ISSN 1872-9142, Vol. 56, nr 3, s. 309-309Artikkel i tidsskrift (Annet vitenskapelig)
  • 43.
    Engberg, Anna E.
    et al.
    Högskolan i Kalmar, Naturvetenskapliga institutionen.
    Rosengren-Holmberg, Jenny
    Högskolan i Kalmar, Naturvetenskapliga institutionen.
    Nicholls, Ian A.
    Högskolan i Kalmar, Naturvetenskapliga institutionen.
    Nilsson Ekdahl, Kristina
    Högskolan i Kalmar, Naturvetenskapliga institutionen.
    Development of novel biomaterial surfaces and evaluation of their hemocompatibility*2008Inngår i: Journal of Molecular Immunology 45, 2008Konferansepaper (Fagfellevurdert)
  • 44.
    Engberg, Anna E.
    et al.
    Högskolan i Kalmar, Naturvetenskapliga institutionen.
    Rosengren-Holmberg, Jenny
    Högskolan i Kalmar, Naturvetenskapliga institutionen.
    Nicholls, Ian A.
    Högskolan i Kalmar, Naturvetenskapliga institutionen.
    Nilsson Ekdahl, Kristina
    Högskolan i Kalmar, Naturvetenskapliga institutionen.
    Development of novel biomaterial surfaces and evaluation of their hemocompatibility2008Konferansepaper (Fagfellevurdert)
  • 45.
    Engberg, Anna E.
    et al.
    Högskolan i Kalmar, Naturvetenskapliga institutionen.
    Rosengren-Holmberg, Jenny P.
    Högskolan i Kalmar, Naturvetenskapliga institutionen.
    Nilsson Ekdahl, Kristina
    Högskolan i Kalmar, Naturvetenskapliga institutionen.
    Nicholls, Ian A.
    Högskolan i Kalmar, Naturvetenskapliga institutionen.
    Synthesis of new polymers and evaluation of their hemocompatibility2009Konferansepaper (Fagfellevurdert)
  • 46.
    Engberg, Anna E.
    et al.
    Högskolan i Kalmar, Naturvetenskapliga institutionen.
    Rosengren-Holmberg, Jenny P
    Högskolan i Kalmar, Naturvetenskapliga institutionen.
    Nilsson, Per H.
    Högskolan i Kalmar, Naturvetenskapliga institutionen.
    Bäck,
    Department of Oncology, Radiology and Clinical Immunology, Section of Clinical Immunology, Rudbeck Laboratory C5, Uppsala University Hospital, SE-751 85 Uppsala, Sweden.
    Mollnes, Tom Eirik
    Institute of Immunology, Rikshospitalet University Hospital, Oslo, Norway,Research Laboratory, Nordland Hospital, Bodø, and University of Tromsø, Norway.
    Nicholls, Ian A.
    Högskolan i Kalmar, Naturvetenskapliga institutionen.
    Nilsson, Bo
    Department of Oncology, Radiology and Clinical Immunology, Section of Clinical Immunology, Rudbeck Laboratory C5, Uppsala University Hospital, SE-751 85 Uppsala, Sweden.
    Nilsson Ekdahl, Kristina
    Högskolan i Kalmar, Naturvetenskapliga institutionen.
    EVALUATION OF THE HEMOCOMPATIBILITY OF NOVEL POLYMERIC MATERIALSManuskript (preprint) (Annet vitenskapelig)
    Abstract [en]

    When a biomaterial surface comes in contact with blood an immediate adsorption of plasma proteins to the surface will occur, and the cascade systems in the blood, such as the complement, coagulation and contact system, will be activated to various degrees. The intensity of this reaction will determine the hemocompatibility of the materials. Here we present an evaluation of the link between the composition, the physico-chemical properties and the protein adsorption properties of six newly synthesized polymers (P1-P6) and the hemocompatibility.The hemocompatibility of the polymeric surfaces was evaluated in human blood plasma and whole blood. Commercially available polyvinylchloride (PVC) was used as reference material. The hemocompatibility of the polymeric surfaces was evaluated with regard to complement activation (C3a and sC5-9 generation) and coagulation activation (platelet loss and TAT-formation) and cytokine productions (27 analytes in multiplex assay) after contact with whole blood. Contact activation was quantified by analyses of FXIIa-C1INH, FXIa-C1INH, and kallikrein-C1INH complexes.Polymers P2 (p<0.05 for C3a), P3, P5 and P6 showed less complement activation, and polymers P1 and P4 (p<0.05 for platelet loss), as well as P5 and P6 showed less coagulation activation compared with reference PVC. Polymers P1-P3 induced activation of the contact system, P3 being the most potent. Secretion of 17 cytokines including chemokines and growth factors were differentially influenced by the polymers, P1 and P3 being significantly (p<0.05) more compatible for five of the analytes.Collectively these data demonstrate that the composition of the polymers clearly leads to different biological properties as a consequence of distinctive physico-chemical properties and protein adsorption patterns.1

  • 47.
    Giovannoli, Cristina
    et al.
    Univ Turin, Italy.
    Passini, Cinzia
    Univ Turin, Italy.
    Di Nardo, Fabio
    Univ Turin, Italy.
    Anfossi, Laura
    Univ Turin, Italy.
    Baggiani, Claudio
    Univ Turin, Italy.
    Nicholls, Ian A.
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för kemi och biomedicin (KOB).
    Affinity Capillary Electrochromatography of Molecularly Imprinted Thin Layers Grafted onto Silica Capillaries Using a Surface-Bound Azo-Initiator and Living Polymerization2018Inngår i: Polymers, ISSN 2073-4360, E-ISSN 2073-4360, Vol. 10, nr 2, artikkel-id 192Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Molecularly imprinted thin layers were prepared in silica capillaries by using two different surface polymerization strategies, the first using 4,4-azobis(4-cyanovaleric acid) as a surface-coupled radical initiator, and the second, S-carboxypropyl-S'-benzyltrithiocarbonate as a reversible addition-fragmentation chain transfer (RAFT) agent in combination with 2,2-azobisisobutyronitrile as a free radical initiator. The ability to generate imprinted thin layers was tested on two different polymerization systems: (i) a 4-vinylpyridine/ethylene dimethacrylate (4VP-EDMA) in methanol-water solution with 2,4,5-trichlorophenoxyacetic acid (2,4,5-T) as a template; and (ii) methacrylic acid/ethylene dimethacrylate (MAA-EDMA) in a chloroform solution with warfarin as the template molecule. The binding properties of the imprinted capillaries were studied and compared with those of the corresponding non-imprinted polymer coated capillaries by injecting the template molecule and by measuring its migration times relative to a neutral and non-retained marker. The role of running buffer hydrophobicity on recognition was investigated by studying the influence of varying buffer acetonitrile concentration. The 2,4,5-T-imprinted capillary showed molecular recognition based on a reversed phase mechanism, with a decrease of the template recognition in the presence of higher acetonitrile content; whereas warfarin-imprinted capillaries showed a bell-shaped trend upon varying the acetonitrile percentage, illustrating different mechanisms underlying imprinted polymer-ligand recognition. Importantly, the results demonstrated the validity of affinity capillary electrochromatography (CEC) to screen the binding properties of imprinted layers.

  • 48.
    Golker, Kerstin
    et al.
    Linnéuniversitetet, Fakultetsnämnden för naturvetenskap och teknik, Institutionen för naturvetenskap, NV.
    Karlsson, Björn C. G.
    Linnéuniversitetet, Fakultetsnämnden för naturvetenskap och teknik, Institutionen för naturvetenskap, NV.
    Olsson, Gustaf D.
    Linnéuniversitetet, Fakultetsnämnden för naturvetenskap och teknik, Institutionen för naturvetenskap, NV.
    Nicholls, Ian A.
    Linnéuniversitetet, Fakultetsnämnden för naturvetenskap och teknik, Institutionen för naturvetenskap, NV.
    Towards Molecular Dynamics-Based Rational Design of Polymeric Recognition Systems2010Konferansepaper (Fagfellevurdert)
    Abstract [en]

    Molecular imprinting is a technique used to design polymeric recognition materials with selectivity for a predetermined structure. The molecular imprinting process generates cavities in the polymer matrix that are complementary in size, shape and functionality to the template-structure. The recognition properties of molecularly imprinted polymers (MIPs) are comparable to those of antibodies and enzymes, which make MIPs utilizable in a wide range of application areas including biomimetic assays and biosensors [1]. Previous studies have shown that the prepolymerization step is central for the establishment of high affinity binding sites in MIPs [2]. However, our understanding of the physical mechanisms underlying MIP formation and template recognition is still limited. With the rapid increase of computational power and the development of suitable software molecular dynamics (MD) simulation methods have become a valuable theoretical tool to aid our understanding of the molecular imprinting process, and even in the development of rational design strategies [2]. Recently the first simulation of a complete prepolymerization mixture was presented [3].

    Here we present 10 ns MD simulations of a series of all-component prepolymerization mixtures. The simulated systems were assembled with different molar ratios using the local anaesthetic bupivacaine as the template, methacrylic acid (MAA) as the functional monomer, ethylene glycol dimethacrylate (EGDMA) as the crosslinker, 2,2’-azobis-(2-methylpropionitrile) (AIBN) as the initiator and toluene as the solvent. The simulations were performed using the AMBER (v. 10.0 UCSF, San Francisco, CA) suite of programs (4) and the GAFF [6] force field. Molecular trajectories were evaluated with radial distribution functions and hydrogen bond analysis.

     

     

    References

    1. Alexander, C.; Andersson, H. S.; Andersson, L. I.; Ansell, R. J.; Kirsch, N.; Nicholls, I. A.; O´Mahony, J.; Whitcombe, J., J. Mol. Recognit. (2006), 19, 106-180
    2. Nicholls, I. A.; Andersson, H. S.; Charlton, C.; Henschel, H.; Karlsson, B. C. G.; Karlsson, J. G.; O´Mahony, J.; Rosengren, A. M.; Rosengren, K. J.; Wikman, S. Biosens. Bioelectron. (2009), 25, 543-552
    3. Karlsson, B. C. G.; O´Mahony, J.; Karlsson, J. G.; Bengtsson, H.; Eriksson, L. A.; Nicholls, I. A. J. Am. Chem. Soc. (2009), 131, 13297-13304
    4. Case, D. A.; Cheatham, T. E.; Darden, T.; Gohlke, H.; Luo, R.; Merz, K. M.; Onufriev, A.; Simmerling, C.; Wang, B.; Woods, R. J. Comput. Chem. (2009), 26, 1668-1688
    5. Wang, J.; Wolf, R. M.; Caldwell, J. W.; Kollman, P. A.; Case, D. A. J. Comput. Chem. (2004), 25, 1157-1174

     

  • 49.
    Golker, Kerstin
    et al.
    Linnéuniversitetet, Fakultetsnämnden för naturvetenskap och teknik, Institutionen för naturvetenskap, NV.
    Karlsson, Björn C. G.
    Linnéuniversitetet, Fakultetsnämnden för naturvetenskap och teknik, Institutionen för naturvetenskap, NV.
    Olsson, Gustaf D.
    Linnéuniversitetet, Fakultetsnämnden för naturvetenskap och teknik, Institutionen för naturvetenskap, NV.
    Nicholls, Ian A.
    Linnéuniversitetet, Fakultetsnämnden för naturvetenskap och teknik, Institutionen för naturvetenskap, NV.
    Towards Molecular Dynamics-Based Rational Design of Synthetic Polymer Recognition Systems2010Konferansepaper (Fagfellevurdert)
    Abstract [en]

    Molecularly imprinted polymers (MIPs) are polymeric receptors with selectivity for a predetermined structure. The molecular imprinting process generates cavities in a synthetic polymer matrix that are complementary in size, shape and functionality to the template. MIPs exhibit recognition properties analogous to their biological counterparts, such as antibodies, and can be utilized in a wide range of application areas [1]. Nonetheless, the physical mechanisms underlying MIP formation and template recognition are still poorly understood. Molecular dynamics (MD) based computer simulations are a valuable theoretical tool which may be used to aid our understanding of the molecular imprinting process, and even for the development of rational design strategies [2]. Recently the first MD simulation of a complete prepolymerization mixture was presented [3].

    In the present work, MD simulations of a series of all-component prepolymerization mixtures were performed, using the local anaesthetic bupivacaine as the template, methacrylic acid (MAA) as the functional monomer, ethylene glycol dimethacrylate (EGDMA) as the crosslinker, 2,2’-azobis-(2-methylpropionitrile) (AIBN) as the initiator and toluene as the solvent. The simulated systems differed in the molar fraction of MAA. Systems were evaluated with radial distribution functions and hydrogen bond analyses. By correlating the results with the rebinding behaviour of a series of synthesized MIPs the importance of the stoichiometry between template, functional monomer and crosslinker was highlighted. The analysis of the MD simulations revealed strong competition for hydrogen bonding between the carbonyl oxygen’s of MAA and EGDMA and the amide proton of bupivacaine. Moreover, the hydrogen bonding contact between EGDMA and bupivacaine remained nearly unaffected by the varied molar fraction MAA in the different systems demonstrating the role of the crosslinker being more important as generally accepted.

     

    References

    [1]             Alexander, C.; Andersson, H. S.; Andersson, L. I.; Ansell, R. J.; Kirsch, N.; Nicholls, I. A.; O´Mahony, J.; Whitcombe, J., J. Mol. Recognit., 19, 106-180 (2006)

    [2]            Nicholls, I. A.; Andersson, H. S.; Charlton, C.; Henschel, H.; Karlsson, B. C. G.; Karlsson, J. G.; O´Mahony, J.; Rosengren, A. M.; Rosengren, K. J.; Wikman, S. Biosens. Bioelectron., 25, 543-552 (2009)

    [3]            Karlsson, B. C. G.; O´Mahony, J.; Karlsson, J. G.; Bengtsson, H.; Eriksson, L. A.; Nicholls, I. A. J. Am. Chem. Soc., 131, 13297-13304 (2009)

  • 50.
    Golker, Kerstin
    et al.
    Linnéuniversitetet, Fakultetsnämnden för naturvetenskap och teknik, Institutionen för naturvetenskap, NV.
    Karlsson, Björn C. G.
    Linnéuniversitetet, Fakultetsnämnden för naturvetenskap och teknik, Institutionen för naturvetenskap, NV.
    Olsson, Gustaf D.
    Linnéuniversitetet, Fakultetsnämnden för naturvetenskap och teknik, Institutionen för naturvetenskap, NV.
    Nicholls, Ian A.
    Linnéuniversitetet, Fakultetsnämnden för naturvetenskap och teknik, Institutionen för naturvetenskap, NV.
    Towards the use of molecular dynamics as a predictive tool in the design of molecularly imprinted polymers2010Konferansepaper (Fagfellevurdert)
    Abstract [en]

    Through the rapid increase in computational power and the development of suitable software, molecular dynamics (MD) has become a promising tool for use in the development of molecularly imprinted polymers (MIPs).1 MD is a computational method based on Newtonian mechanics, which enables the simultaneous simulation of thousands of discrete molecules, and can be used to establish the states of the molecular species present in MIP-prepolymerization mixtures. As detailed understanding of the molecular basis for formation of high affinity MIP sites is still lacking and the physical mechanism underlying specific recognition is still a matter of debate, the use of MD as a tool to investigate MIP-prepolymerization mixtures is highly motivated.1 Recently the first MD simulation of an all-component prepolymerization mixture was presented, which gave a detailed picture of the underlying monomer-template interactions important for the “molecular memory” in MIPs.2

    Here, we present results obtained from a series of MD simulations representing all-component MIP/REF prepolymerization mixtures assembled with differences in stoichiometries of functional and crosslinking monomer. In these mixtures, the local anaesthetic drug bupivacaine was used as a template, methacrylic acid as the functional monomer, ethylene dimethacrylate as crosslinking monomer, 2,2’-azobis-(2-methylpropionitrile) as the initiator and toluene as the solvent. Bupivacaine complexation in each system was evaluated with radial distribution functions and hydrogen bond analyses. By correlating the results with the rebinding behaviour of a series of synthesized bupivacaine-MIPs, the relationship between the degree of crosslinking and MIP-performance was highlighted.

    [1] Nicholls, I. A.; Andersson, H. S.; Charlton, C.; Henschel, H.; Karlsson, B. C. G.; Karlsson, J. G.; O´Mahony, J.; Rosengren, A. M.; Rosengren, K. J.; Wikman, S. Biosens. Bioelectron., 25, 543-552 (2009)

    [2] Karlsson, B. C. G.; O´Mahony, J.; Karlsson, J. G.; Bengtsson, H.; Eriksson, L. A.; Nicholls, I. A. J. Am. Chem. Soc., 131, 13297-13304 (2009)

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