Chris Hendrix

Structure-activity relationship of short-chain sphingoid bases as inhibitors of sphingosine kinase.

Short-chain sphinganine analogues 8, 9, 18, and 19, as well as 3-fluoro-sphingosine analogues 25 and 26 were synthesized. Their potential as sphingosine kinase inhibitors was investigated, in combination with previously synthesized sphingosine and fluorinated sphinganine analogues.

SYNTHESIS AND PAIRING PROPERTIES OF OLIGONUCLEOTIDES CONTAINING 3-HYDROXY-4-HYDROXYMETHYL-1-CYCLOHEXANYL NUCLEOSIDES

Cyclohexanyl nucleic acid (CNA) represents a novel enantioselective Watson–Crick base-pairing system. Homochiral oligomers of equivalent chirality show antiparallel Watson–Crick pairing, while those of opposite sense do not. D-CNA hybridizes with natural nucleic acids, preferentially with RNA. A conformational change involving chair inversion is expected to occur upon duplex formation (A→B).

Synthesis of fluorinated sphinganine and dihydroceramide analogues

With the aim of uncovering inhibitors of dihydroceramide desaturase and ceramide synthase and studying their substrate specificity, the synthesis of short-chain 3-fluorosphinganine and 3-fluorodihydroceramide analogues was effected. The synthesis starts from the known alkynols 1 and 10, respectively, and from the Garner aldehyde 15. The key step is the introduction of a fluorine atom using diethylaminosulfur trifluoride, which proceeds efficiently for erythro-alcohols 2 and 16, but gives rise to cyclization reactions for threo compounds 11 and 17.

DNA-Binding Ligands from Peptide Libraries Containing Unnatural Amino Acids

Combinatorial chemistry with a newly-developed screening procedure using complementary fluorescein- and rhodamine-labelled oligonucleotides (below) has been used to select peptide dsDNA binding ligands. A high structure–affinity relationship of the dsDNA-binding unnatural peptide was observed.

Synthesis and apoptogenic activity of fluorinated ceramide and dihydroceramide analogues

Short-chain 3-fluoro-(dihydro)ceramide analogues are synthesized from L-serine using diethylaminosulfur trifluoride (DAST) as fluorinating agent. The apoptogenic activity of these compounds was measured in three different cell lines and compared with their hydroxylated counterparts.

Synthesis of Alanine and Proline Amino Acids with Amino or Guanidinium Substitution on the Side Chain

Abstract Competitive binding of peptides containing basic amino acids to disrupt or prevent the Tat–TAR interaction could result in diminished transcription as well as translation and hence constitutes an alternative way of controlling HIV replication. Therefore, we synthesized guanidinium and amino containing amino acids, based on a proline or an alanine scaffold. The introduction of the guanidinium moiety was best accomplished using 1H-pyrazole-1-carboxamidine hydrochloride, with Pmc used for its protection. The absence of racemization, maintained throughout the whole synthesis, was confirmed by chiral purity determination. These building blocks were smoothly incorporated into oligopeptides, which proved their suitability for use in a combinatorial approach for selecting TAR binding ligands.

Synthesis of the Anticodon HairpintRNAfMet ContainingN-{[9-(β-D-Ribofuranosyl)-9H-purin-6-yl]carbamoyl}-L-threonine (=N6-{{[(1S,2R)-1-Carboxy-2-hydroxypropyl]amino}carbonyl}adenosine, t6A)

As part of our studies on the structure of yeast tRNAfMet, we investigated the incorporation of N-{[9-(β-D-ribofuranosyl)-9H-purin-6-yl]carbamoyl}-L-threonine (t6A) in the loop of a RNA 17-mer hairpin. The carboxylic function of the L-threonine moiety of t6A was protected with a 2-(4-nitrophenyl)ethyl group, and a (tert-butyl)dimethylsilyl group was used for the protection of its secondary OH group. The 2′-OH function of the standard ribonucleotide building blocks was protected with a [(triisopropylsilyl)oxy]methyl group. Removal of the base-labile protecting groups of the final RNA with 1,8-diazabicyclo[5.4.0]undec-7-ene (DBU) and then with MeNH2 was done under carefully controlled conditions to prevent hydrolysis of the carbamate function, leading to loss of the L-threonine moiety.

Selection of new sequence-selective unnatural peptides binding to double-stranded deoxyribonucleic acids (dsDNA) by means of a gel-retardation experiment for library analysis

Previously, we developed a methodology for the solid-phase screening of peptide libraries for interaction with double-stranded deoxyribonucleic acids (dsDNA). In the search for new and more-potent DNA ligands, we investigated the strategy of solution-phase screening of chemical libraries consisting of unnatural oligopeptides. After synthesis of the selected amino acid building blocks, libraries were constructed with the general structure Ac-Arg-Ual-Sar-X1-X2-X3-Arg-NH2, where X represents each of twelve unnatural or natural amino acids. Optimization of the sequence of binding peptides was performed with an iterative deconvolution procedure. Selection of interacting peptides was carried out in solution by means of gel-retardation experiments, starting with libraries of 144 compounds. A 14-base-pair double-stranded DNA fragment was chosen as the target. After several cycles of synthesis and screening of libraries and individual peptides, an oligopeptide was selected with an apparent dissociation constant of 9⋅10−5 M, as determined by gel-retardation experiments. This peptide was studied by NMR spectroscopy. A certain degree of conformational pre-organization of the peptides was shown by temperature-dependent circular-dichroism experiments. Finally, DNase-I-footprinting studies indicated a preferential interaction with a 6-base-pair mixed sequence 5′-CTGCAT-3′. This study demonstrates that gel-shift experiments can be used for the solution-phase screening of library mixtures of peptides against dsDNA. In general, this technique allows the selection of new sequence-selective dsDNA-interacting molecules. Furthermore, novel dsDNA-binding unnatural oligopeptides were developed with affinities in the 0.1 mM range.

Synthesis of 3′-fluoromethylthio-, 3′-fluoromethylsulfinyl- and 3′-fluoromethylsulfonyl-substituted 3′-deoxythymidine

3′- Deoxy- 3′-(fluoromethylthio)thymidine 2 is synthesized from 5′-O-benzoyl-3′-deoxy-3′-(methylsulfinyl)thymidine 9 by using DAST. 5′-O- Benzoyl-3′-deoxy-3′-(fluoromethylthio)thymidine is used as starting material for the synthesis of the sulfoxide 3 and the sulfone 4. Both sulfoxides 3A and 3B show a C3′-endo sugar conformation.