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  • 1.
    Blom, Magnus
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Synthetical Organic Chemistry.
    Light-Triggered Conformational Switches for Modulation of Molecular Recognition: Applications for Peptidomimetics and Supramolecular Systems2015Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    The main focus of this thesis is on photochemical modulation of molecular recognition in various host-guest systems. This involves the design, synthesis and integration of light-triggered conformational switches into peptidomimetic guests and molecular tweezer hosts. The impact of the switches on guest and host structures has been assessed by spectroscopic and computational conformational analysis. Effects of photochemical structure modulation on molecular recognition in protein-ligand and supramolecular host-guest systems are discussed.

    Phototriggerable peptidomimetic inhibitors of the enzyme M. tuberculosis ribonucleotide reductase (RNR) were obtained by incorporation of a stilbene based amino acid moiety into oligopeptides between 3-9 residues long (Paper I). Interstrand hydrogen bond probability in the E and Z forms of the peptidomimetics was used as a tool for predicting conformational preferences. Considerable differences in inhibitory potency for the E and Z photoisomers were demonstrated in a binding assay.

    In order to advance the concept of photomodulable inhibitors, synthetic routes towards amino acid derivatives based on the more rigid stiff-stilbene chromophore were developed (Paper II).  The effect of E-Z isomerization on the conformational properties of peptidomimetic inhibitors incorporating the stiff-stilbene chromophore was also assessed computationally (Paper III). It was indicated that inhibitors with the more rigid amino acid derivative should display larger conformational divergence between photoisomers than corresponding stilbene derivatives.

    Bisporphyrin tweezers with enediyne and stiff-stilbene spacers have been synthesized, and the conformational characteristics imposed by the spacers have been studied and compared to a glycoluril linked tweezer. The effects of spacers on tweezer binding of diamine guests and helicity induction by chiral guests have been investigated (Paper IV). Connections between spacer flexibility and host-guest binding strength have been established. The structural properties of the stiff-stilbene spaced tweezer made it particularly susceptible to helicity induction by both monotopic and bitopic chiral guests. Finally, the possibility of photochemical bite-size variation of tweezers with photoswitchable spacers has been assessed. Initial studies have shown that photoisomerization of the tweezers is possible without photochemical decomposition. Conformational analyses indicate that isomerization should impact binding characteristics of the tweezers to a significant extent (Paper V).

    List of papers
    1. Phototriggerable peptidomimetics for the inhibition of Mycobacterium turberculosis ribonucleotide reductase by targeting protein-protein binding
    Open this publication in new window or tab >>Phototriggerable peptidomimetics for the inhibition of Mycobacterium turberculosis ribonucleotide reductase by targeting protein-protein binding
    Show others...
    2015 (English)In: Organic and biomolecular chemistry, ISSN 1477-0520, E-ISSN 1477-0539, Vol. 13, no 9, p. 2612-2621Article in journal (Refereed) Published
    Abstract [en]

    Incorporation of an artificial amino acid 2 with a stilbene chromophore into peptidomimetics with three to nine amino acids yields phototriggerable candidates for inhibition of the binding between the R1 and R2 subunits of the M. tuberculosis ribonucleotide reductase (RNR). Interstrand hydrogen bond probability was used as a guideline for predicting conformational preferences of the photoisomers. Binding of these inhibitors has been rationalized by docking studies with the R1 unit. Significant differences in binding of the photoisomers were observed. For the shorter peptidomimetics, stronger binding of the Z isomer might indicate hydrophobic interactions between the stilbene chromophore and the binding site.

    National Category
    Organic Chemistry Medicinal Chemistry
    Research subject
    Chemistry with specialization in Organic Chemistry; Medicinal Chemistry
    Identifiers
    urn:nbn:se:uu:diva-239491 (URN)10.1039/C4OB01926A (DOI)000350144600018 ()25580895 (PubMedID)
    Funder
    Swedish Research Council
    Available from: 2014-12-28 Created: 2014-12-28 Last updated: 2018-01-11Bibliographically approved
    2. Synthesis and characterization of photoswitchable stiff-stilbene based amino acid derivatives
    Open this publication in new window or tab >>Synthesis and characterization of photoswitchable stiff-stilbene based amino acid derivatives
    (English)Manuscript (preprint) (Other academic)
    Abstract [en]

    Synthetic routes towards the Boc-protected amino acids 1 and 2 incorporating the stiff stilbene chromophore via the corresponding indanone carboxylic acids have been devised. Crucial steps are a reductive McMurry coupling of the indanone carboxylic acids, yielding stiff stilbene dicarboxylic acid esters. Hydrolysis to the monoester and conversion to the azides, followed by a Curtius rearrangement afforded the Boc-protected amino acid ester 1.

    Keywords
    Peptidomimetics
    National Category
    Organic Chemistry
    Research subject
    Chemistry with specialization in Organic Chemistry
    Identifiers
    urn:nbn:se:uu:diva-267829 (URN)
    Funder
    Swedish Research Council, 621-2012-3379
    Available from: 2015-11-27 Created: 2015-11-27 Last updated: 2016-01-13
    3. Photoswitchable peptidomimetics with a stiff-stilbene chromophore for inhibition of Mycobacterium tuberculosis RNR
    Open this publication in new window or tab >>Photoswitchable peptidomimetics with a stiff-stilbene chromophore for inhibition of Mycobacterium tuberculosis RNR
    (English)Manuscript (preprint) (Other academic)
    Abstract [en]

    Peptidomimetics incorporating two amino acids 1 and 2 with a stiff stilbene chromophore have been screened by a computational study and compared to a previously investigated analog 3 with stilbene chromophore. The effect of E-Z isomerization of the chromophores on the conformational properties of the petidomimetics was assessed via the frequency of hydrogen bonding between the two peptide strands attached to either side of the chromophore. Substantial differences between the three amino acids were thus indicated, in line with the anticipated effect of chromophore rigidity variation.

    Keywords
    Peptidomimetics, conformational analysis
    National Category
    Organic Chemistry
    Research subject
    Chemistry with specialization in Organic Chemistry
    Identifiers
    urn:nbn:se:uu:diva-267830 (URN)
    Funder
    Swedish Research Council, 621-2012-3379
    Available from: 2015-11-27 Created: 2015-11-27 Last updated: 2016-01-13
    4. Synthesis and Properties of Bis-Porphyrin Molecular Tweezers: Effects of Spacer Flexibility on Binding and Supramolecular Chirogenesis
    Open this publication in new window or tab >>Synthesis and Properties of Bis-Porphyrin Molecular Tweezers: Effects of Spacer Flexibility on Binding and Supramolecular Chirogenesis
    Show others...
    2016 (English)In: Molecules, ISSN 1420-3049, E-ISSN 1420-3049, Vol. 21, no 1Article in journal (Refereed) Published
    Abstract [en]

    Abstract: Ditopic binding of various dinitrogen compounds to three bisporphyrin molecular tweezers with spacers of varying conformational rigidity, incorporating the planar ene-diyne (1), the helical stiff stilbene (2), or the semirigid glycoluril motif fused to  the porphyrins (3) are compared. Binding constants Ka = 10^4 to 10^6 M^-1 reveal subtle  differences between these tweezers, that are discussed in terms of porphyrin dislocation  modes. Exciton coupled circular dichroism (ECCD) of complexes with chiral dinitrogen  guests provides experimental evidence for the conformational properties of the tweezers. The results are further supported and rationalized by conformational analysis.

    Keywords
    Bisporphyrin tweezers, metalloporphyrins, porphyrinoids, host-guest chemistry, supramolecular chemistry, chirogenesis, chirality transfer, exciton coupled circular dichroism, conformational analysis
    National Category
    Organic Chemistry Engineering and Technology
    Research subject
    Chemistry with specialization in Organic Chemistry; Engineering Science with specialization in Nanotechnology and Functional Materials
    Identifiers
    urn:nbn:se:uu:diva-267826 (URN)10.3390/molecules21010016 (DOI)000369485600001 ()
    Funder
    Swedish Research Council, 621-2012-3379Swedish Research Council, 621-2011-4423
    Available from: 2015-11-27 Created: 2015-11-27 Last updated: 2017-12-01Bibliographically approved
    5. Photomodulable bis-porphyrin molecular tweezers as dynamic host systems for diamine guests
    Open this publication in new window or tab >>Photomodulable bis-porphyrin molecular tweezers as dynamic host systems for diamine guests
    Show others...
    (English)Manuscript (preprint) (Other academic)
    Abstract [en]

    Bisporphyrin molecular tweezers with an enediyne (1) or a stiff stilbene (2) photoswitchable spacer are proposed as systems for modulation of bitopic binding to diamine guests via E/Z photoisomerization. The photoisomerization has been monitored by UV-Vis and 1H NMR spectroscopy and occurs without side reactions such as Bergman cyclization. Possible applications are rationalized in terms of competitive binding involving monoamine/diamine mixtures, and are supported by conformational analysis of the envisioned host-guest complexes. Binding dynamics for conformationally flexible guests show significantly different performance of aliphatic 1,w-diamine guests with varying N-N distance.

    Keywords
    Bisporphyrin tweezers, supramolecular chemistry, photochemistry
    National Category
    Organic Chemistry
    Research subject
    Chemistry with specialization in Organic Chemistry
    Identifiers
    urn:nbn:se:uu:diva-267833 (URN)
    Funder
    Swedish Research Council, 621-2012-3379
    Available from: 2015-11-27 Created: 2015-11-27 Last updated: 2016-01-13
  • 2.
    Blom, Magnus
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Synthetical Organic Chemistry.
    Huang, Hao
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Nanotechnology and Functional Materials.
    Gogoll, Adolf
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Biochemistry and Organic Chemistry, Organic Chemistry I.
    Photoswitchable peptidomimetics with a stiff-stilbene chromophore for inhibition of Mycobacterium tuberculosis RNRManuscript (preprint) (Other academic)
    Abstract [en]

    Peptidomimetics incorporating two amino acids 1 and 2 with a stiff stilbene chromophore have been screened by a computational study and compared to a previously investigated analog 3 with stilbene chromophore. The effect of E-Z isomerization of the chromophores on the conformational properties of the petidomimetics was assessed via the frequency of hydrogen bonding between the two peptide strands attached to either side of the chromophore. Substantial differences between the three amino acids were thus indicated, in line with the anticipated effect of chromophore rigidity variation.

  • 3.
    Blom, Magnus
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Synthetical Organic Chemistry.
    Huang, Hao
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Nanotechnology and Functional Materials.
    Gogoll, Adolf
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Synthetical Organic Chemistry.
    Synthesis and characterization of photoswitchable stiff-stilbene based amino acid derivativesManuscript (preprint) (Other academic)
    Abstract [en]

    Synthetic routes towards the Boc-protected amino acids 1 and 2 incorporating the stiff stilbene chromophore via the corresponding indanone carboxylic acids have been devised. Crucial steps are a reductive McMurry coupling of the indanone carboxylic acids, yielding stiff stilbene dicarboxylic acid esters. Hydrolysis to the monoester and conversion to the azides, followed by a Curtius rearrangement afforded the Boc-protected amino acid ester 1.

  • 4.
    Blom, Magnus
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Synthetical Organic Chemistry.
    Norrehed, Sara
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Synthetical Organic Chemistry.
    Andersson, Claes-Henrik
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Synthetical Organic Chemistry.
    Huang, Hao
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Nanotechnology and Functional Materials.
    Light, Mark E.
    Department of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, U.K.
    Bergquist, Jonas
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Analytical Chemistry.
    Grennberg, Helena
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Physical Organic Chemistry.
    Gogoll, Adolf
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Synthetical Organic Chemistry.
    Synthesis and Properties of Bis-Porphyrin Molecular Tweezers: Effects of Spacer Flexibility on Binding and Supramolecular Chirogenesis2016In: Molecules, ISSN 1420-3049, E-ISSN 1420-3049, Vol. 21, no 1Article in journal (Refereed)
    Abstract [en]

    Abstract: Ditopic binding of various dinitrogen compounds to three bisporphyrin molecular tweezers with spacers of varying conformational rigidity, incorporating the planar ene-diyne (1), the helical stiff stilbene (2), or the semirigid glycoluril motif fused to  the porphyrins (3) are compared. Binding constants Ka = 10^4 to 10^6 M^-1 reveal subtle  differences between these tweezers, that are discussed in terms of porphyrin dislocation  modes. Exciton coupled circular dichroism (ECCD) of complexes with chiral dinitrogen  guests provides experimental evidence for the conformational properties of the tweezers. The results are further supported and rationalized by conformational analysis.

  • 5.
    Blom, Magnus
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Synthetical Organic Chemistry.
    Olsson, Sandra
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Synthetical Organic Chemistry.
    Norrehed, Sara
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Synthetical Organic Chemistry.
    Andersson, Claes-Henrik
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Physical Organic Chemistry.
    Grennberg, Helena
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Physical Organic Chemistry.
    Gogoll, Adolf
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Biochemistry and Organic Chemistry, Organic Chemistry I.
    Photomodulable bis-porphyrin molecular tweezers as dynamic host systems for diamine guestsManuscript (preprint) (Other academic)
    Abstract [en]

    Bisporphyrin molecular tweezers with an enediyne (1) or a stiff stilbene (2) photoswitchable spacer are proposed as systems for modulation of bitopic binding to diamine guests via E/Z photoisomerization. The photoisomerization has been monitored by UV-Vis and 1H NMR spectroscopy and occurs without side reactions such as Bergman cyclization. Possible applications are rationalized in terms of competitive binding involving monoamine/diamine mixtures, and are supported by conformational analysis of the envisioned host-guest complexes. Binding dynamics for conformationally flexible guests show significantly different performance of aliphatic 1,w-diamine guests with varying N-N distance.

  • 6.
    Karlsson, Christoffer
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC.
    Blom, Magnus
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Synthetical Organic Chemistry.
    Johansson, Miranda
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Synthetical Organic Chemistry.
    Jansson, Anna M.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Scifo, Enzo
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Karlén, Anders
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry, Organic Pharmaceutical Chemistry.
    Govender, Thavendran
    Catalysis and Peptide Research Unit, University of KwaZulu Natal, South Africa.
    Gogoll, Adolf
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Synthetical Organic Chemistry.
    Phototriggerable peptidomimetics for the inhibition of Mycobacterium turberculosis ribonucleotide reductase by targeting protein-protein binding2015In: Organic and biomolecular chemistry, ISSN 1477-0520, E-ISSN 1477-0539, Vol. 13, no 9, p. 2612-2621Article in journal (Refereed)
    Abstract [en]

    Incorporation of an artificial amino acid 2 with a stilbene chromophore into peptidomimetics with three to nine amino acids yields phototriggerable candidates for inhibition of the binding between the R1 and R2 subunits of the M. tuberculosis ribonucleotide reductase (RNR). Interstrand hydrogen bond probability was used as a guideline for predicting conformational preferences of the photoisomers. Binding of these inhibitors has been rationalized by docking studies with the R1 unit. Significant differences in binding of the photoisomers were observed. For the shorter peptidomimetics, stronger binding of the Z isomer might indicate hydrophobic interactions between the stilbene chromophore and the binding site.

  • 7.
    Olsson, Sandra K.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Organic Chemistry.
    Benito Perez, Oscar
    Universitat de Barcelona.
    Blom, Magnus
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Organic Chemistry.
    Gogoll, Adolf
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Organic Chemistry.
    Effect of Ring Size on Photoisomerization Properties of Stiff Stilbene macrocyclesManuscript (preprint) (Other academic)
    Abstract [en]

    A series of stiff stilbene macrocycles have been studied in order to investigate the possible impact of macrocycle ring size on their photo-dynamic properties. The results show that reducing the ring size counteracts the photoisomerization ability of the macrocycles. However, even the smallest macrocycle studied (stiff stilbene subunits linked by a six carbon chain) showed some degree of isomerization when irradiated. DFT calculations of the energy differences between the E- and Z-isomers show the same trend as the experimental results. Interestingly the DFT study highlights that the energy difference between the E- and Z-isomers of even the largest macrocycle (linked by a twelve carbon chain) is significantly higher than that of the stiff stilbene unit itself. This indicates that a flexible chain may significantly affect the efficiency of photoisomerizations.

  • 8.
    Olsson, Sandra K.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Organic Chemistry.
    Schäfer, Clara
    Friedrich-Alexander-University Erlangen-Nürnberg.
    Blom, Magnus
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Organic Chemistry.
    Gogoll, Adolf
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Organic Chemistry.
    Exciton-Coupled Circular Dichroism Characterization of Monotopically Binding Guests in Host-Guest Complexes with a Bis(zinc porphyrin) Tweezer2018In: ChemPlusChem, ISSN 2192-6506, Vol. 83, p. 1169-1178Article in journal (Refereed)
    Abstract [en]

    A stiff-stilbene-linked bisporphyrin tweezer with inherent helicity was used for exciton-coupled circular dichroism (ECCD) characterization of a series of monotopically binding amine guest molecules. CD signals were observed for a variety of monoamines at relatively low tweezer/amine (host/guest) ratios between 1 :10 to 1: 70. For the amines producing the most intense CD signals, a binding stoichiometry of 1:2 was found. A likely explanation is the presence of guest-guest interactions in the complexes. This is supported by the correlation observed between CD signal intensity and magnitude of possible noncovalent binding between the guests, which can be divided into three groups showing no, moderate and strong response, respectively. Further support for this rationalization comes from molecular modelling.

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