Dmytro S. Radchenko

Bicyclic Conformationally Restricted Diamines

CONTENTS

4-Fluoro-2,4-methanoproline.

The first fluorinated analogue of the naturally occurring 2,4-methanoproline, 4-fluoro-2,4-methanoproline, has been synthesized in five steps from commercially available methyl 2-fluoroacrylate through a photochemical cyclization as a key step in generating a 2-azabicyclo[2.1.1]hexane skeleton.

Design, synthesis, and application of a trifluoromethylated phenylalanine analogue as a label to study peptides by solid-state 19F NMR spectroscopy.

F NMR spectroscopy is a powerful technique to resolve the structure and dynamics of peptides and proteins. The large gyromagnetic ratio, the absence of a biological background, the high sensitivity of the chemical shift to the local environment, and the spin of =2 make fluorine an attractive nucleus for NMR spectroscopy. Solid-state F NMR spectroscopy of macroscopically oriented samples, in particular, is used to determine the structure, alignment, and dynamics of membrane-bound peptides under quasi-native conditions. To this aim, suitable fluorine-labeled amino acids have to be incorporated selectively into the polypeptide backbone. However, they have to meet several strict criteria: 1) they must be conformationally constrained to place the F reporter group in a well-defined position relative to the peptide backbone; 2) they must be compatible with standard procedures for solid-phase peptide synthesis (SPPS); 3) they must not perturb the native structure or function of the peptide. These criteria preclude the use of virtually all readily available fluorinated analogues of proteinogenic amino acids, as because of their conformational flexibility they do not fulfill criterion 1. Recently, several trifluoromethyl-substituted compounds 1–4 have been designed and applied as labels for solid-state F NMR spectroscpy, specifically to replace either bulky aliphatic amino acids (1), or proline (2), or serine/ threonine (3), or a-aminoisobutyric acid (4) in membrane-active peptides. However, the aromatic phenylalanine analogues 5 and 6, which have also been explored, showed significant disadvantages, as they racemized under standard Fmoc SPPS conditions (Fmoc = 9-fluorenylmethyloxycarbonyl) and thus did not meet criterion 3. Purification of the target peptides was problematic, and in some cases even impossible. Furthermore, analysis of the chemical shift anisotropy of the F atom in 5 had to take into account the side chain c1 angle and required complicated referencing. [10] We thus aimed to expand the scope of available labels and report herein the rational design, synthesis, and validation of a novel aromatic label for solid-state F NMR spectroscopy to replace phenylalanine.

Cyclobutane-derived diamines: synthesis and molecular structure.

Cyclobutane diamines (i.e., cis- and trans-1,3-diaminocyclobutane, 6-amino-3-azaspiro[3.3]heptane, and 3,6-diaminospiro[3.3]heptane) are considered as promising sterically constrained diamine building blocks for drug discovery. An approach to the syntheses of their Boc-monoprotected derivatives has been developed aimed at the preparation of multigram amounts of the compounds. These novel synthetic schemes exploit classical malonate alkylation chemistry for the construction of cyclobutane rings. The conformational preferences of the cyclobutane diamine derivatives have been evaluated by X-ray diffraction and compared with the literature data on sterically constrained diamines, which are among the constituents of commercially available drugs.

Conformationally restricted nonchiral pipecolic acid analogues.

Practical syntheses of 2-azabicyclo[3.1.1]heptane-1-carboxylic (2,4-methanopipecolic), 2-azabicyclo[2.2.2]octane-1-carboxylic (2,5-ethanopipecolic), and 9-azabicyclo[3.3.1]nonane-1-carboxylic (2,6-propanopipecolic) acids are reported. The synthetic schemes are short (five, seven, and five steps, respectively) and result in reasonably high yields of the title compounds. The key step in the syntheses is the tandem Strecker reaction and intramolecular nucleophilic cyclization of ketones possessing a leaving group at the delta-position.

Delivering Structural Information on the Polar Face of Membrane‐Active Peptides: 19F‐NMR Labels with a Cationic Side Chain

Conformationally constrained non-racemizing trifluoromethyl-substituted lysine isosteres [(E)- and (Z)-TCBLys] with charged side chains are presented as a new type of 19 F-NMR labels for peptide studies. Design of the labels, their synthesis, incorporation into peptides and experimental demonstration of their application for solid state NMR studies of membrane-active peptides are described. A series of fluorine-labeled analogues of the helical amphipathic antimicrobial peptide PGLa(Nle) was obtained, in which different lysine residues in the original peptide sequence were replaced, one at a time, by either (E)- or (Z)-TCBLys. Antimicrobial activities of the synthesized analogues were practically the same as those of the parent peptide. The structural and orientational parameters of the helical PGLa(Nle) peptide in model bilayers, as determined using the novel labels confirmed and refined the previously known structure. (E)- and (Z)-TCBLys, as a set of cationic 19 F-NMR labels, were shown to deliver structural information about the charged face of amphipathic peptides by solid state 19 F-NMR, previously inaccessible by this method.

Synthesis of 2-azaspiro[3.3]heptane-derived amino acids: ornitine and GABA analogues

Synthesis of 6-amino-2-azaspiro[3.3]heptane-6-carboxylic acid and 2-azaspiro[3.3]heptane-6-carboxylic acid was performed. Both four-membered rings in the spirocyclic scaffold were constructed by subsequent ring closure of corresponding 1,3-bis-electrophiles at 1,1-C- or 1,1-N-bis-nucleophiles. The two novel amino acids were added to the family of the sterically constrained amino acids for the use in chemistry, biochemistry, and drug design.

Synthesis and Structural Analysis of Angular Monoprotected Diamines Based on Spiro[3.3]heptane Scaffold

The synthesis of all stereoisomers of spiro[3.3]heptane-1,6-diamines suitably protected for use as building blocks in drug discovery is reported. Structural analysis revealed the similarity between the spiro[3.3]heptane and cyclohexane scaffolds. Comparison of the distance between functional groups and their spatial orientation proved that (1S,4r,6R)- and (1R,4r,6S)-1,6-disubstituted spiro[3.3]heptanes can be considered as restricted surrogates of cis-1,4-disubstituted cyclohexane derivatives. Similarly, (1S,4s,6R)- and (1R,4s,6S)-1,6-disubstituted spiro[3.3]heptanes are the restricted surrogates of trans-1,3-disubstituted cyclohexanes. Such replacement can be recommended for use in optimization of ADME parameters of lead compounds in drug discovery.

Conformationally restricted glutamic acid analogues: stereoisomers of 1-aminospiro[3.3]heptane-1,6-dicarboxylic acid

All four stereoisomers of the title compound (1a–d) were prepared, starting from a common precursor, 3-oxocyclobutanecarboxylic acid. Lewis acid-catalyzed rearrangement of a 8-oxadispiro[2.0.3.1]octane-6-carboxylic acid derivative was used as the key synthetic step to construct the suitably functionalized spiro[3.3]heptane skeleton. A stabilized oxaphosphetane intermediate of the Wittig reaction was detected along the synthetic route. Separation of the diastereomeric intermediates allowed each target compound to be obtained as a single stereoisomer. The target compounds are all analogues of the glutamic acid; they mimic glutamate in a large array of restricted conformations, which might be used in mechanistic studies or in a systematic search for biologically active compounds.

Expedient Synthesis of cis- and trans-3-Aminocyclobutanecarboxylic Acids

Abstract An expedient approach to cis- and trans-3-aminocyclobutanecarboxylic acids was developed starting from 1,1-cyclobutanedicarboxylic acid. Stereochemistry of the title compounds was established by nuclear Overhauser effect spectroscopy experiments.