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  1. Abstract

    Determination of the solution conformation of both small organic molecules and peptides in water remains a substantial hurdle in using NMR solution conformations to guide drug design due to the lack of easy to use alignment media. Herein we report the design of a flexible compressible chemically cross‐linked poly‐4‐acrylomorpholine gel that can be used for the alignment of both small molecules and cyclic peptides in water. To test the new gel, residual dipolar couplings (RDCs) andJ‐coupling constants were used in the configurational analysis of strychnine hydrochloride, a molecule that has been studied extensively in organic solvents as well as a small cyclic peptide that is known to form an α‐helix in water. The conformational ensembles for each molecule with the best fit to the data are reported. Identification of minor conformers in water that cannot easily be determined by conventional NOE measurements will facilitate the use of RDC experiments in structure‐based drug design.

     
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  2. Abstract

    Determination of the solution conformation of both small organic molecules and peptides in water remains a substantial hurdle in using NMR solution conformations to guide drug design due to the lack of easy to use alignment media. Herein we report the design of a flexible compressible chemically cross‐linked poly‐4‐acrylomorpholine gel that can be used for the alignment of both small molecules and cyclic peptides in water. To test the new gel, residual dipolar couplings (RDCs) andJ‐coupling constants were used in the configurational analysis of strychnine hydrochloride, a molecule that has been studied extensively in organic solvents as well as a small cyclic peptide that is known to form an α‐helix in water. The conformational ensembles for each molecule with the best fit to the data are reported. Identification of minor conformers in water that cannot easily be determined by conventional NOE measurements will facilitate the use of RDC experiments in structure‐based drug design.

     
    more » « less
  3. Abstract

    We present a method to use long‐range CH coupling constants to derive the correct diastereoisomer from the molecular constitution of small molecules. A set of 792JCHand3JCHvalues collected from a single HSQMBC experiment on a sample of strychnine were used in the CASE‐3D (computer‐assisted 3D structure elucidation) protocol. In addition to the most commonly used3JCHcoupling constants, the subset of 322JCHvalues alone showed an excellent degree of configuration selection. The study is mainly based on comparison of DFT‐calculated2,3JCHvalues with experimental ones, critical for the case of2JCH. But the configuration selection also works well using3JCHvalues predicted from a semi‐empirical Karplus‐based equation limited to H−C−C−C fragments. The robustness, shown using strychnine as a proof of concept, makes theJ‐based CASE‐3D analysis a viable option for the application in fields such as peptide and carbohydrate research, organic synthesis, natural‐product identification and analysis, as well as medicinal chemistry.

     
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  4. Abstract

    We present a method to use long‐range CH coupling constants to derive the correct diastereoisomer from the molecular constitution of small molecules. A set of 792JCHand3JCHvalues collected from a single HSQMBC experiment on a sample of strychnine were used in the CASE‐3D (computer‐assisted 3D structure elucidation) protocol. In addition to the most commonly used3JCHcoupling constants, the subset of 322JCHvalues alone showed an excellent degree of configuration selection. The study is mainly based on comparison of DFT‐calculated2,3JCHvalues with experimental ones, critical for the case of2JCH. But the configuration selection also works well using3JCHvalues predicted from a semi‐empirical Karplus‐based equation limited to H−C−C−C fragments. The robustness, shown using strychnine as a proof of concept, makes theJ‐based CASE‐3D analysis a viable option for the application in fields such as peptide and carbohydrate research, organic synthesis, natural‐product identification and analysis, as well as medicinal chemistry.

     
    more » « less